I have now invested some time to install Atmel Studio on a Windows 7 partition, and to check how Atmel Studio writes to eeprom.

Short Summary
-------------
- Installing and getting started with Atmel Studio is a pain in the
  neck if you are used to nice avrdude and to installing rpm packages
  (and, why does Studio use -v for specifying options with 2 perfectly
  different semantics in a single line?).

- The effort to install Atmel Studio is nevertheless worth while, even
  if, later, you only use avrdude: it allows you to get the latest
  firmware update for your jtagice3 (for me that meant an upgrade from
  firmware version 1.37 to version 2.21).

- However, the firmware upgrade does not solve the problem discussed
  here.

- Failures on single-byte eeprom write operations do not only occur
  with Avrdude, but also with Atmel Studio - maybe somewhat less
  frequently than with Avrdude, but so often that the jtagice3 is
  practically useless if you want to write to eeprom positions.

- It looks like the problem is not necessarily due to the
  implementation of Avrdude (or Atmel Studio) but could just as well
  be a flaw in the implementation of the firmware of the jtagice3.

- To be repeated here: corresponding single-byte operations work
  perfectly when using a JTAG ICE mkII - nevertheless, I will now
  confection a new target board with a new processor to make sure that
  the problem is not a due to the specific processor I am using.


Detailed description
--------------------
In the attachment, I join a file into which I have pasted the console I/O for both a single-byte read and a single-byte write, and both for Avrdude and for Atmel Studio. Atmel Studio only has a simple -v option, which does not provide much information on how Studio proceeds when it
writes to eeprom.


Juergen
Opening interactive avrdude session (with -vvvv debug option)
=============================================================

<harms@pcjuergen ~> avrdude -vvvv -p AT90CAN128 -c jtag3 -P usb -t

avrdude: Version 6.0.1, compiled on Dec 14 2013 at 14:56:08
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "/etc/avrdude/avrdude.conf"
         User configuration file is "/home/harms/.avrduderc"
         User configuration file does not exist or is not a regular file, 
skipping

         Using Port                    : usb
         Using Programmer              : jtag3
avrdude: jtag3_open()
avrdude: usbdev_open(): Found JTAGICE3, serno: J30200021991
avrdude: jtag3_getsync()
avrdude: Sending sign-on command: 
avrdude: jtag3_send(): sending 3 bytes
avrdude: Sent: . [0e] . [00] . [00] . [00] . [01] . [10] . [00] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [00] . [00] . [01] . [80] . [00] 
avrdude: jtag3_recv(): Got message seqno 0 (command_sequence == 0)

Raw message:
01  80  00  
[general] OK
         AVR Part                      : AT90CAN128
         Chip Erase delay              : 9000 us
         PAGEL                         : PD7
         BS2                           : PA0
         RESET disposition             : dedicated
         RETRY pulse                   : SCK
         serial program mode           : yes
         parallel program mode         : yes
         Timeout                       : 200
         StabDelay                     : 100
         CmdexeDelay                   : 25
         SyncLoops                     : 32
         ByteDelay                     : 0
         PollIndex                     : 3
         PollValue                     : 0x53
         Memory Detail                 :

                                  Block Poll               Page                 
      Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  
MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- 
----- ---------
           eeprom        65    20     8    0 no       4096    8      0  9000  
9000 0xff 0xff
                                  Block Poll               Page                 
      Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  
MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- 
----- ---------
           flash         65     6   256    0 yes    131072  256    512  4500  
4500 0xff 0xff
                                  Block Poll               Page                 
      Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  
MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- 
----- ---------
           lfuse          0     0     0    0 no          1    0      0  9000  
9000 0x00 0x00
                                  Block Poll               Page                 
      Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  
MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- 
----- ---------
           hfuse          0     0     0    0 no          1    0      0  9000  
9000 0x00 0x00
                                  Block Poll               Page                 
      Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  
MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- 
----- ---------
           efuse          0     0     0    0 no          1    0      0  9000  
9000 0x00 0x00
                                  Block Poll               Page                 
      Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  
MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- 
----- ---------
           lock           0     0     0    0 no          1    0      0  9000  
9000 0x00 0x00
                                  Block Poll               Page                 
      Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  
MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- 
----- ---------
           calibration    0     0     0    0 no          1    0      0     0    
 0 0x00 0x00
                                  Block Poll               Page                 
      Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  
MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- 
----- ---------
           signature      0     0     0    0 no          3    0      0     0    
 0 0x00 0x00

         Programmer Type : JTAGICE3
         Description     : Atmel AVR JTAGICE3 in JTAG mode
avrdude: jtag3_getparm()
avrdude: Sending get parameter (scope 0x01, section 0, parm 0) command: 
avrdude: jtag3_send(): sending 6 bytes
avrdude: Sent: . [0e] . [00] . [01] . [00] . [01] . [02] . [00] . [00] . [00] . 
[05] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [01] . [00] . [01] . [84] . [01] . [02] . [01] % [25] . 
[bf] . [00] . [00] 
avrdude: jtag3_recv(): Got message seqno 1 (command_sequence == 1)

Raw message:
01  84  01  02  01  25  bf  00  00  
[general] Data returned:
0x01 0x02 0x01 0x25 0xbf 0x00 0x00 
avrdude: Sending get info (serial number) command: 
avrdude: jtag3_send(): sending 4 bytes
avrdude: Sent: . [0e] . [00] . [02] . [00] . [00] . [00] . [00] . [81] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [02] . [00] . [00] . [81] . [00] J [4a] 3 [33] 0 [30] 2 
[32] 0 [30] 0 [30] 0 [30] 2 [32] 1 [31] 9 [39] 9 [39] 1 [31] 
avrdude: jtag3_recv(): Got message seqno 2 (command_sequence == 2)

Raw message:
00  81  00  4a  33  30  32  30  30  30  32  31  39  39  31  
[info] Info returned:
\000J30200021991
         ICE hardware version: 2
         ICE firmware version: 1.37 (rel. 191)
         Serial number   : J30200021991
avrdude: jtag3_getparm()
avrdude: Sending get parameter (scope 0x01, section 1, parm 0) command: 
avrdude: jtag3_send(): sending 6 bytes
avrdude: Sent: . [0e] . [00] . [03] . [00] . [01] . [02] . [00] . [01] . [00] . 
[02] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [03] . [00] . [01] . [84] . [01] . [0f] . [13] . [00] 
avrdude: jtag3_recv(): Got message seqno 3 (command_sequence == 3)

Raw message:
01  84  01  0f  13  00  
[general] Data returned:
0x01 0x0f 0x13 0x00 
         Vtarget         : 4.88 V
avrdude: jtag3_getparm()
avrdude: Sending get parameter (scope 0x12, section 1, parm 32) command: 
avrdude: jtag3_send(): sending 6 bytes
avrdude: Sent: . [0e] . [00] . [04] . [00] . [12] . [02] . [00] . [01]   [20] . 
[02] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [04] . [00] . [12] . [84] . [00] . [e8] . [03] . [00] 
avrdude: jtag3_recv(): Got message seqno 4 (command_sequence == 4)

Raw message:
12  84  00  e8  03  00  
[AVR] Data returned:
0x00 0xe8 0x03 0x00 
         JTAG clock megaAVR/program: 1000 kHz
avrdude: jtag3_getparm()
avrdude: Sending get parameter (scope 0x12, section 1, parm 33) command: 
avrdude: jtag3_send(): sending 6 bytes
avrdude: Sent: . [0e] . [00] . [05] . [00] . [12] . [02] . [00] . [01] ! [21] . 
[02] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [05] . [00] . [12] . [84] . [00] . [e8] . [03] . [00] 
avrdude: jtag3_recv(): Got message seqno 5 (command_sequence == 5)

Raw message:
12  84  00  e8  03  00  
[AVR] Data returned:
0x00 0xe8 0x03 0x00 
         JTAG clock megaAVR/debug:   1000 kHz
avrdude: jtag3_getparm()
avrdude: Sending get parameter (scope 0x12, section 1, parm 48) command: 
avrdude: jtag3_send(): sending 6 bytes
avrdude: Sent: . [0e] . [00] . [06] . [00] . [12] . [02] . [00] . [01] 0 [30] . 
[02] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [06] . [00] . [12] . [84] . [00] . [e8] . [03] . [00] 
avrdude: jtag3_recv(): Got message seqno 6 (command_sequence == 6)

Raw message:
12  84  00  e8  03  00  
[AVR] Data returned:
0x00 0xe8 0x03 0x00 
         JTAG clock Xmega: 1000 kHz
avrdude: jtag3_getparm()
avrdude: Sending get parameter (scope 0x12, section 1, parm 49) command: 
avrdude: jtag3_send(): sending 6 bytes
avrdude: Sent: . [0e] . [00] . [07] . [00] . [12] . [02] . [00] . [01] 1 [31] . 
[02] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [07] . [00] . [12] . [84] . [00] . [e8] . [03] . [00] 
avrdude: jtag3_recv(): Got message seqno 7 (command_sequence == 7)

Raw message:
12  84  00  e8  03  00  
[AVR] Data returned:
0x00 0xe8 0x03 0x00 
         PDI clock Xmega : 1000 kHz

avrdude: jtag3_getparm()
avrdude: Sending get parameter (scope 0x01, section 0, parm 1) command: 
avrdude: jtag3_send(): sending 6 bytes
avrdude: Sent: . [0e] . [00] . [08] . [00] . [01] . [02] . [00] . [00] . [01] . 
[02] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [08] . [00] . [01] . [84] . [01] . [01] % [25] . [00] 
avrdude: jtag3_recv(): Got message seqno 8 (command_sequence == 8)

Raw message:
01  84  01  01  25  00  
[general] Data returned:
0x01 0x01 0x25 0x00 
avrdude: jtag3_setparm()
avrdude: Sending set parameter (scope 0x12, section 0, parm 0) command: 
avrdude: jtag3_send(): sending 7 bytes
avrdude: Sent: . [0e] . [00] . [09] . [00] . [12] . [01] . [00] . [00] . [00] . 
[01] . [02] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [09] . [00] . [12] . [80] . [00] 
avrdude: jtag3_recv(): Got message seqno 9 (command_sequence == 9)

Raw message:
12  80  00  
[AVR] OK
avrdude: jtag3_setparm()
avrdude: Sending set parameter (scope 0x12, section 0, parm 1) command: 
avrdude: jtag3_send(): sending 7 bytes
avrdude: Sent: . [0e] . [00] . [0a] . [00] . [12] . [01] . [00] . [00] . [01] . 
[01] . [01] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [0a] . [00] . [12] . [80] . [00] 
avrdude: jtag3_recv(): Got message seqno 10 (command_sequence == 10)

Raw message:
12  80  00  
[AVR] OK
avrdude: jtag3_setparm()
avrdude: Sending set parameter (scope 0x12, section 1, parm 0) command: 
avrdude: jtag3_send(): sending 7 bytes
avrdude: Sent: . [0e] . [00] . [0b] . [00] . [12] . [01] . [00] . [01] . [00] . 
[01] . [04] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [0b] . [00] . [12] . [80] . [00] 
avrdude: jtag3_recv(): Got message seqno 11 (command_sequence == 11)

Raw message:
12  80  00  
[AVR] OK
avrdude: jtag3_initialize(): trying to set JTAG daisy-chain info to 0,0,0,0
avrdude: jtag3_setparm()
avrdude: Sending set parameter (scope 0x12, section 1, parm 1) command: 
avrdude: jtag3_send(): sending 10 bytes
avrdude: Sent: . [0e] . [00] . [0c] . [00] . [12] . [01] . [00] . [01] . [01] . 
[04] . [00] . [00] . [00] . [00] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [0c] . [00] . [12] . [80] . [00] 
avrdude: jtag3_recv(): Got message seqno 12 (command_sequence == 12)

Raw message:
12  80  00  
[AVR] OK
avrdude: jtag3_setparm()
avrdude: Sending set parameter (scope 0x12, section 2, parm 0) command: 
avrdude: jtag3_send(): sending 37 bytes
avrdude: Sent: . [0e] . [00] . [0d] . [00] . [12] . [01] . [00] . [02] . [00] . 
[1f] . [00] . [01] . [00] . [00] . [02] . [00] . [00] . [00] . [00] . [00] . 
[00] . [fe] . [00] . [00] . [00] . [00] . [00] . [10] . [08] . [03] . [01] . 
[00] . [00] . [00] 1 [31] " [22] ! [21] . [1f]   [20] W [57] . [00] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [0d] . [00] . [12] . [80] . [00] 
avrdude: jtag3_recv(): Got message seqno 13 (command_sequence == 13)

Raw message:
12  80  00  
[AVR] OK
avrdude: Sending AVR sign-on command: 
avrdude: jtag3_send(): sending 4 bytes
avrdude: Sent: . [0e] . [00] . [0e] . [00] . [12] . [10] . [00] . [00] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [0e] . [00] . [12] . [84] . [00] ? [3f] . [10] x [78] . 
[09] . [00] 
avrdude: jtag3_recv(): Got message seqno 14 (command_sequence == 14)

Raw message:
12  84  00  3f  10  78  09  00  
[AVR] Data returned:
0x00 0x3f 0x10 0x78 0x09 0x00 
avrdude: JTAG ID returned: 0x3f 0x10 0x78 0x09
avrdude: AVR device initialized and ready to accept instructions

Reading |                                                    | 0% 0.00savrdude: 
jtag3_read_byte(.., signature, 0x0, ...)
avrdude: Sending enter progmode command: 
avrdude: jtag3_send(): sending 3 bytes
avrdude: Sent: . [0e] . [00] . [0f] . [00] . [12] . [15] . [00] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [0f] . [00] . [12] . [80] . [00] 
avrdude: jtag3_recv(): Got message seqno 15 (command_sequence == 15)

Raw message:
12  80  00  
[AVR] OK
avrdude: Sending read memory command: 
avrdude: jtag3_send(): sending 12 bytes
avrdude: Sent: . [0e] . [00] . [10] . [00] . [12] ! [21] . [00] . [b4] . [00] . 
[00] . [00] . [00] . [03] . [00] . [00] . [00] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [10] . [00] . [12] . [84] . [00] . [1e] . [97] . [81] . 
[00] 
avrdude: jtag3_recv(): Got message seqno 16 (command_sequence == 16)

Raw message:
12  84  00  1e  97  81  00  
[AVR] Data returned:
0x00 0x1e 0x97 0x81 0x00 
avrdude: jtag3_read_byte(.., signature, 0x1, ...)
Reading | #################                                  | 33% 
0.07savrdude: jtag3_read_byte(.., signature, 0x2, ...)
Reading | ################################################## | 100% 0.07s

avrdude: Device signature = 0x1e9781
avrdude: jtag3_read_byte(.., lfuse, 0x0, ...)
avrdude: Sending read memory command: 
avrdude: jtag3_send(): sending 12 bytes
avrdude: Sent: . [0e] . [00] . [11] . [00] . [12] ! [21] . [00] . [b2] . [00] . 
[00] . [00] . [00] . [01] . [00] . [00] . [00] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [11] . [00] . [12] . [84] . [00] . [ef] . [00] 
avrdude: jtag3_recv(): Got message seqno 17 (command_sequence == 17)

Raw message:
12  84  00  ef  00  
[AVR] Data returned:
0x00 0xef 0x00 
avrdude: safemode read 1, lfuse value: ef
avrdude: jtag3_read_byte(.., lfuse, 0x0, ...)
avrdude: Sending read memory command: 
avrdude: jtag3_send(): sending 12 bytes
avrdude: Sent: . [0e] . [00] . [12] . [00] . [12] ! [21] . [00] . [b2] . [00] . 
[00] . [00] . [00] . [01] . [00] . [00] . [00] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [12] . [00] . [12] . [84] . [00] . [ef] . [00] 
avrdude: jtag3_recv(): Got message seqno 18 (command_sequence == 18)

Raw message:
12  84  00  ef  00  
[AVR] Data returned:
0x00 0xef 0x00 
avrdude: safemode read 2, lfuse value: ef
avrdude: jtag3_read_byte(.., lfuse, 0x0, ...)
avrdude: Sending read memory command: 
avrdude: jtag3_send(): sending 12 bytes
avrdude: Sent: . [0e] . [00] . [13] . [00] . [12] ! [21] . [00] . [b2] . [00] . 
[00] . [00] . [00] . [01] . [00] . [00] . [00] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [13] . [00] . [12] . [84] . [00] . [ef] . [00] 
avrdude: jtag3_recv(): Got message seqno 19 (command_sequence == 19)

Raw message:
12  84  00  ef  00  
[AVR] Data returned:
0x00 0xef 0x00 
avrdude: safemode read 3, lfuse value: ef
avrdude: safemode: lfuse reads as EF
avrdude: jtag3_read_byte(.., hfuse, 0x0, ...)
avrdude: Sending read memory command: 
avrdude: jtag3_send(): sending 12 bytes
avrdude: Sent: . [0e] . [00] . [14] . [00] . [12] ! [21] . [00] . [b2] . [01] . 
[00] . [00] . [00] . [01] . [00] . [00] . [00] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [14] . [00] . [12] . [84] . [00] . [11] . [00] 
avrdude: jtag3_recv(): Got message seqno 20 (command_sequence == 20)

Raw message:
12  84  00  11  00  
[AVR] Data returned:
0x00 0x11 0x00 
avrdude: safemode read 1, hfuse value: 11
avrdude: jtag3_read_byte(.., hfuse, 0x0, ...)
avrdude: Sending read memory command: 
avrdude: jtag3_send(): sending 12 bytes
avrdude: Sent: . [0e] . [00] . [15] . [00] . [12] ! [21] . [00] . [b2] . [01] . 
[00] . [00] . [00] . [01] . [00] . [00] . [00] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [15] . [00] . [12] . [84] . [00] . [11] . [00] 
avrdude: jtag3_recv(): Got message seqno 21 (command_sequence == 21)

Raw message:
12  84  00  11  00  
[AVR] Data returned:
0x00 0x11 0x00 
avrdude: safemode read 2, hfuse value: 11
avrdude: jtag3_read_byte(.., hfuse, 0x0, ...)
avrdude: Sending read memory command: 
avrdude: jtag3_send(): sending 12 bytes
avrdude: Sent: . [0e] . [00] . [16] . [00] . [12] ! [21] . [00] . [b2] . [01] . 
[00] . [00] . [00] . [01] . [00] . [00] . [00] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [16] . [00] . [12] . [84] . [00] . [11] . [00] 
avrdude: jtag3_recv(): Got message seqno 22 (command_sequence == 22)

Raw message:
12  84  00  11  00  
[AVR] Data returned:
0x00 0x11 0x00 
avrdude: safemode read 3, hfuse value: 11
avrdude: safemode: hfuse reads as 11
avrdude: jtag3_read_byte(.., efuse, 0x0, ...)
avrdude: Sending read memory command: 
avrdude: jtag3_send(): sending 12 bytes
avrdude: Sent: . [0e] . [00] . [17] . [00] . [12] ! [21] . [00] . [b2] . [02] . 
[00] . [00] . [00] . [01] . [00] . [00] . [00] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [17] . [00] . [12] . [84] . [00] . [f5] . [00] 
avrdude: jtag3_recv(): Got message seqno 23 (command_sequence == 23)

Raw message:
12  84  00  f5  00  
[AVR] Data returned:
0x00 0xf5 0x00 
avrdude: safemode read 1, efuse value: f5
avrdude: jtag3_read_byte(.., efuse, 0x0, ...)
avrdude: Sending read memory command: 
avrdude: jtag3_send(): sending 12 bytes
avrdude: Sent: . [0e] . [00] . [18] . [00] . [12] ! [21] . [00] . [b2] . [02] . 
[00] . [00] . [00] . [01] . [00] . [00] . [00] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [18] . [00] . [12] . [84] . [00] . [f5] . [00] 
avrdude: jtag3_recv(): Got message seqno 24 (command_sequence == 24)

Raw message:
12  84  00  f5  00  
[AVR] Data returned:
0x00 0xf5 0x00 
avrdude: safemode read 2, efuse value: f5
avrdude: jtag3_read_byte(.., efuse, 0x0, ...)
avrdude: Sending read memory command: 
avrdude: jtag3_send(): sending 12 bytes
avrdude: Sent: . [0e] . [00] . [19] . [00] . [12] ! [21] . [00] . [b2] . [02] . 
[00] . [00] . [00] . [01] . [00] . [00] . [00] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [19] . [00] . [12] . [84] . [00] . [f5] . [00] 
avrdude: jtag3_recv(): Got message seqno 25 (command_sequence == 25)

Raw message:
12  84  00  f5  00  
[AVR] Data returned:
0x00 0xf5 0x00 
avrdude: safemode read 3, efuse value: f5
avrdude: safemode: efuse reads as F5


Reading a byte in an interactive Avrdude session (-vvvv option)
===============================================================

avrdude> read eeprom 0x014 1
>>> read eeprom 0x014 1 
avrdude: jtag3_read_byte(.., eeprom, 0x14, ...)
avrdude: Sending read memory command: 
avrdude: jtag3_send(): sending 12 bytes
avrdude: Sent: . [0e] . [00] . [1a] . [00] . [12] ! [21] . [00] . [b1] . [10] . 
[00] . [00] . [00] . [08] . [00] . [00] . [00] 
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [1a] . [00] . [12] . [84] . [00] . [a8] . [00] . [ff] . 
[ff] . [10] . [ff] . [02] . [ff] . [00] 
avrdude: jtag3_recv(): Got message seqno 26 (command_sequence == 26)

Raw message:
12  84  00  a8  00  ff  ff  10  ff  02  ff  00  
[AVR] Data returned:
0x00 0xa8 0x00 0xff 0xff 0x10 0xff 0x02 0xff 0x00 
0014  10                                                |.               |




Failed write of a byte in an interactive Avrdude session (-vvvv option)
=======================================================================

avrdude> write eeprom 0x014 0x11
>>> write eeprom 0x014 0x11                                                     
avrdude: jtag3_write_byte(.., eeprom, 0x14, ...)                                
avrdude: jtag3_read_byte(.., eeprom, 0x14, ...)                                 
avrdude: Sending read memory command:                                           
avrdude: jtag3_send(): sending 12 bytes                                         
avrdude: Sent: . [0e] . [00] . [1b] . [00] . [12] ! [21] . [00] . [b1] . [10] . 
[00] . [00] . [00] . [08] . [00] .. [00]                                        
                                  
avrdude: jtag3_recv():                                                          
avrdude: Recv: . [0e] . [1b] . [00] . [12] . [84] . [00] . [a8] . [00] . [ff] . 
[ff] . [10] . [ff] . [02] . [ff] .
avrdude: jtag3_recv(): Got message seqno 27 (command_sequence == 27)            
                                                                                
Raw message:                                                                    
12  84  00  a8  00  ff  ff  10  ff  02  ff  00                                  
[AVR] Data returned:                                                            
0x00 0xa8 0x00 0xff 0xff 0x10 0xff 0x02 0xff 0x00                               
avrdude: jtag3_paged_write(.., eeprom, 8, 8)                                    
avrdude: jtag3_paged_write(): block_size at addr 16 is 8                        
avrdude: Sending write memory command:                                          
avrdude: jtag3_send(): sending 21 bytes                                         
avrdude: Sent: . [0e] . [00] . [1c] . [00] . [12] # [23] . [00] . [b1] . [10] . 
[00] . [00] . [00] . [08] . [00] .. [00] . [00] . [a8] . [00] . [ff] . [ff] . 
[11] . [ff] . [02] . [ff]           
avrdude: jtag3_recv():                                                          
avrdude: Recv: . [0e] . [1c] . [00] . [12] . [80] . [00]                        
avrdude: jtag3_recv(): Got message seqno 28 (command_sequence == 28)            
                                                                                
Raw message:                                                                    
12  80  00                                                                      
[AVR] OK                                                                        
avrdude: jtag3_read_byte(.., eeprom, 0x14, ...)                                 
avrdude: Sending read memory command:                                           
avrdude: jtag3_send(): sending 12 bytes                                         
avrdude: Sent: . [0e] . [00] . [1d] . [00] . [12] ! [21] . [00] . [b1] . [10] . 
[00] . [00] . [00] . [08] . [00] .. [00]                                        
                                  
avrdude: jtag3_recv():
avrdude: Recv: . [0e] . [1d] . [00] . [12] . [84] . [00] . [a8] . [00] . [ff] . 
[ff] . [10] . [ff] . [02] . [ff] .
avrdude: jtag3_recv(): Got message seqno 29 (command_sequence == 29)

Raw message:
12  84  00  a8  00  ff  ff  10  ff  02  ff  00  
[AVR] Data returned:
0x00 0xa8 0x00 0xff 0xff 0x10 0xff 0x02 0xff 0x00 
avrdude (write): error writing 0x11 at 0x00014 cell=0x10



Reading a byte with Atmel Studio (with debug option)
====================================================

C:\Users\Juergen\Documents>atprogram -v -t jtagice3 -i jtag -d at90can128 read 
-ee -s 1 -o 0x14
[DEBUG] Starting execution of "read"
[DEBUG] Starting process 'C:\Program Files (x86)\Atmel\Atmel Studio 
6.1\atbackend\atbackend.exe'
[DEBUG] Connecting to TCP:127.0.0.1:49332
[INFO] Connected to jtagicemk3, fw version: 2.21
[INFO] Firmware check OK
:0100140010DB
:00000001FF

[DEBUG] Command "read" finished with return code 0
[DEBUG] Exit successfully.



Failed write of a byte with Atmel Studio (with debug option)
============================================================

C:\Users\Juergen\Documents>atprogram -v -t jtagice3 -i jtag -d at90can128 write 
-ee -v -o 0x15 --values 0x37
[DEBUG] Starting execution of "write"
[DEBUG] Starting process 'C:\Program Files (x86)\Atmel\Atmel Studio 
6.1\atbackend\atbackend.exe'
[DEBUG] Connecting to TCP:127.0.0.1:49354
[INFO] Connected to jtagicemk3, fw version: 2.21
[INFO] Firmware check OK
[DEBUG] Writing eeprom...
[DEBUG] Writing 1 byte(s) to offset 21
[DEBUG] Verifying write...
An error occured executing a command (write):
Verification failed!
[DEBUG] Exit successfully.
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