OK I I ran the update twice in /opt/scripts/tools and got the Already up to 
date message(it updated the first time).

Now when I run the script ./beaglebone-black-make-microSD-flasher-from-eMMC.sh 
I get this in seriall output.  

U-Boot SPL 2016.03-dirty (Apr 19 2016 - 15:43:26)
Trying to boot from MMC
bad magic


U-Boot 2016.03-dirty (Apr 19 2016 - 15:43:26 -0700)

       Watchdog enabled
I2C:   ready
DRAM:  512 MiB
Reset Source: Power-on reset has occurred.
MMC:   OMAP SD/MMC: 0, OMAP SD/MMC: 1
Using default environment

Net:   <ethaddr> not set. Validating first E-fuse MAC
cpsw, usb_ether
Press SPACE to abort autoboot in 2 seconds
switch to partitions #0, OK
mmc0 is current device
Scanning mmc 0:1...
gpio: pin 56 (gpio 56) value is 0
gpio: pin 55 (gpio 55) value is 0
gpio: pin 54 (gpio 54) value is 0
gpio: pin 53 (gpio 53) value is 1
switch to partitions #0, OK
mmc0 is current device
gpio: pin 54 (gpio 54) value is 1
Checking for: /uEnv.txt ...
Checking for: /boot.scr ...
Checking for: /boot/boot.scr ...
Checking for: /boot/uEnv.txt ...
gpio: pin 55 (gpio 55) value is 1
1066 bytes read in 16 ms (64.5 KiB/s)
Loaded environment from /boot/uEnv.txt
debug: [dtb=am335x-boneblack-emmc-overlay.dtb] ...
Using: dtb=am335x-boneblack-emmc-overlay.dtb ...
Checking if uname_r is set in /boot/uEnv.txt...
gpio: pin 56 (gpio 56) value is 1
Running uname_boot ...
loading /boot/vmlinuz-4.4.16-bone-rt-r11 ...
7617496 bytes read in 440 ms (16.5 MiB/s)
loading /boot/dtbs/4.4.16-bone-rt-r11/am335x-boneblack-emmc-overlay.dtb ...
54722 bytes read in 39 ms (1.3 MiB/s)
loading /boot/initrd.img-4.4.16-bone-rt-r11 ...
5445661 bytes read in 320 ms (16.2 MiB/s)
debug: [console=ttyO0,115200n8 bone_capemgr.enable_partno=BB-APA-01,BB-ADC 
root=UUID=e4315bf8-7c53-4964-bfab-1bba46c3c8ba ro rootfstype=ext4 rootwait 
init=/opt/scripts/tools/eMMC/init-eMMC-flasher-v3.sh] ...
debug: [bootz 0x82000000 0x88080000:53181d 0x88000000] ...
Kernel image @ 0x82000000 [ 0x000000 - 0x743bd8 ]
## Flattened Device Tree blob at 88000000
   Booting using the fdt blob at 0x88000000
   Loading Ramdisk to 8face000, end 8ffff81d ... OK
   Loading Device Tree to 8fabd000, end 8facd5c1 ... OK

Starting kernel ...

[    0.000000] Booting Linux on physical CPU 0x0
[    0.000000] Initializing cgroup subsys cpuset
[    0.000000] Initializing cgroup subsys cpu
[    0.000000] Initializing cgroup subsys cpuacct
[    0.000000] Linux version 4.4.16-bone-rt-r11 
(root@a5-imx6q-wandboard-2gb) (gcc version 4.9.2 (Debian 4.9.2-10) ) #1 
PREEMPT RT Tue Aug 2 19:38:19 UTC 2016
[    0.000000] CPU: ARMv7 Processor [413fc082] revision 2 (ARMv7), 
cr=50c5387d
[    0.000000] CPU: PIPT / VIPT nonaliasing data cache, VIPT aliasing 
instruction cache
[    0.000000] Machine model: TI AM335x BeagleBone Black
[    0.000000] cma: Reserved 24 MiB at 0x9e800000
[    0.000000] Memory policy: Data cache writeback
[    0.000000] CPU: All CPU(s) started in SVC mode.
[    0.000000] AM335X ES2.1 (sgx neon )
[    0.000000] Built 1 zonelists in Zone order, mobility grouping on. 
 Total pages: 129920
[    0.000000] Kernel command line: console=ttyO0,115200n8 
bone_capemgr.enable_partno=BB-APA-01,BB-ADC 
root=UUID=e4315bf8-7c53-4964-bfab-1bba46c3c8ba ro rootfstype=ext4 rootwait 
init=/opt/scripts/tools/eMMC/init-eMMC-flasher-v3.sh
[    0.000000] PID hash table entries: 2048 (order: 1, 8192 bytes)
[    0.000000] Dentry cache hash table entries: 65536 (order: 6, 262144 
bytes)
[    0.000000] Inode-cache hash table entries: 32768 (order: 5, 131072 
bytes)
[    0.000000] Memory: 475976K/524288K available (7146K kernel code, 852K 
rwdata, 3652K rodata, 472K init, 914K bss, 23736K reserved, 24576K 
cma-reserved, 0K highmem)
[    0.000000] Virtual kernel memory layout:
[    0.000000]     vector  : 0xffff0000 - 0xffff1000   (   4 kB)
[    0.000000]     fixmap  : 0xffc00000 - 0xfff00000   (3072 kB)
[    0.000000]     vmalloc : 0xe0800000 - 0xff800000   ( 496 MB)
[    0.000000]     lowmem  : 0xc0000000 - 0xe0000000   ( 512 MB)
[    0.000000]     pkmap   : 0xbfe00000 - 0xc0000000   (   2 MB)
[    0.000000]     modules : 0xbf800000 - 0xbfe00000   (   6 MB)
[    0.000000]       .text : 0xc0008000 - 0xc0a93c9c   (10800 kB)
[    0.000000]       .init : 0xc0a94000 - 0xc0b0a000   ( 472 kB)
[    0.000000]       .data : 0xc0b0a000 - 0xc0bdf35c   ( 853 kB)
[    0.000000]        .bss : 0xc0be2000 - 0xc0cc6994   ( 915 kB)
[    0.000000] SLUB: HWalign=64, Order=0-3, MinObjects=0, CPUs=1, Nodes=1
[    0.000000] Preemptible hierarchical RCU implementation.
[    0.000000] Build-time adjustment of leaf fanout to 32.
[    0.000000] NR_IRQS:16 nr_irqs:16 16
[    0.000000] IRQ: Found an INTC at 0xfa200000 (revision 5.0) with 128 
interrupts
[    0.000000] OMAP clockevent source: timer2 at 24000000 Hz
[    0.000013] sched_clock: 32 bits at 24MHz, resolution 41ns, wraps every 
89478484971ns
[    0.000025] clocksource: timer1: mask: 0xffffffff max_cycles: 
0xffffffff, max_idle_ns: 79635851949 ns
[    0.000033] OMAP clocksource: timer1 at 24000000 Hz
[    0.000198] Console: colour dummy device 80x30
[    0.000350] WARNING: Your 'console=ttyO0' has been replaced by 'ttyS0'
[    0.000352] This ensures that you still see kernel messages. Please
[    0.000354] update your kernel commandline.
[    0.089111] Calibrating delay loop... 996.14 BogoMIPS (lpj=4980736)
[    0.089116] pid_max: default: 32768 minimum: 301
[    0.089231] Security Framework initialized
[    0.089237] Yama: becoming mindful.
[    0.089266] AppArmor: AppArmor disabled by boot time parameter
[    0.089428] Mount-cache hash table entries: 1024 (order: 0, 4096 bytes)
[    0.089435] Mountpoint-cache hash table entries: 1024 (order: 0, 4096 
bytes)
[    0.090191] Initializing cgroup subsys io
[    0.090210] Initializing cgroup subsys memory
[    0.090242] Initializing cgroup subsys devices
[    0.090255] Initializing cgroup subsys freezer
[    0.090267] Initializing cgroup subsys net_cls
[    0.090277] Initializing cgroup subsys perf_event
[    0.090286] Initializing cgroup subsys net_prio
[    0.090296] Initializing cgroup subsys pids
[    0.090392] CPU: Testing write buffer coherency: ok
[    0.090398] ftrace: allocating 33011 entries in 65 pages
[    0.172669] Setting up static identity map for 0x800081c0 - 0x8000820c
[    0.177265] devtmpfs: initialized
[    0.192680] VFP support v0.3: implementor 41 architecture 3 part 30 
variant c rev 3
[    0.204450] omap_hwmod: tptc0 using broken dt data from edma
[    0.204589] omap_hwmod: tptc1 using broken dt data from edma
[    0.204712] omap_hwmod: tptc2 using broken dt data from edma
[    0.209542] omap_hwmod: debugss: _wait_target_disable failed
[    0.264728] clocksource: jiffies: mask: 0xffffffff max_cycles: 
0xffffffff, max_idle_ns: 19112604462750000 ns
[    0.266799] xor: measuring software checksum speed
[    0.359142]    arm4regs  :  1222.400 MB/sec
[    0.459092]    8regs     :  1094.400 MB/sec
[    0.559089]    32regs    :  1154.000 MB/sec
[    0.659087]    neon      :  1685.200 MB/sec
[    0.659096] xor: using function: neon (1685.200 MB/sec)
[    0.659132] pinctrl core: initialized pinctrl subsystem
[    0.660925] NET: Registered protocol family 16
[    0.663604] DMA: preallocated 256 KiB pool for atomic coherent 
allocations
[    0.668579] OMAP GPIO hardware version 0.1
[    0.678244] No ATAGs?
[    0.678274] hw-breakpoint: debug architecture 0x4 unsupported.
[    0.879279] raid6: int32x1  gen()   264 MB/s
[    1.049183] raid6: int32x1  xor()   247 MB/s
[    1.219179] raid6: int32x2  gen()   374 MB/s
[    1.389190] raid6: int32x2  xor()   282 MB/s
[    1.559196] raid6: int32x4  gen()   388 MB/s
[    1.729090] raid6: int32x4  xor()   266 MB/s
[    1.899103] raid6: int32x8  gen()   357 MB/s
[    2.069125] raid6: int32x8  xor()   233 MB/s
[    2.239108] raid6: neonx1   gen()  1449 MB/s
[    2.409098] raid6: neonx1   xor()   846 MB/s
[    2.579105] raid6: neonx2   gen()  1878 MB/s
[    2.749097] raid6: neonx2   xor()  1131 MB/s
[    2.919089] raid6: neonx4   gen()  1985 MB/s
[    3.089110] raid6: neonx4   xor()  1200 MB/s
[    3.259091] raid6: neonx8   gen()  1210 MB/s
[    3.429095] raid6: neonx8   xor()   671 MB/s
[    3.429103] raid6: using algorithm neonx4 gen() 1985 MB/s
[    3.429111] raid6: .... xor() 1200 MB/s, rmw enabled
[    3.429117] raid6: using intx1 recovery algorithm
[    3.430900] edma 49000000.edma: Legacy memcpy is enabled, things might 
not work
[    3.437385] edma 49000000.edma: TI EDMA DMA engine driver
[    3.441554] SCSI subsystem initialized
[    3.442197] usbcore: registered new interface driver usbfs
[    3.442264] usbcore: registered new interface driver hub
[    3.442370] usbcore: registered new device driver usb
[    3.442829] omap_i2c 44e0b000.i2c: could not find pctldev for node 
/ocp/l4_wkup@44c00000/scm@210000/pinmux@800/pinmux_i2c0_pins, deferring 
probe
[    3.442875] omap_i2c 4819c000.i2c: could not find pctldev for node 
/ocp/l4_wkup@44c00000/scm@210000/pinmux@800/pinmux_i2c2_pins, deferring 
probe
[    3.442974] media: Linux media interface: v0.10
[    3.443037] Linux video capture interface: v2.00
[    3.443128] pps_core: LinuxPPS API ver. 1 registered
[    3.443136] pps_core: Software ver. 5.3.6 - Copyright 2005-2007 Rodolfo 
Giometti <giome...@linux.it>
[    3.443168] PTP clock support registered
[    3.443755] omap-mailbox 480c8000.mailbox: omap mailbox rev 0x400
[    3.444900] NetLabel: Initializing
[    3.444913] NetLabel:  domain hash size = 128
[    3.444919] NetLabel:  protocols = UNLABELED CIPSOv4
[    3.444984] NetLabel:  unlabeled traffic allowed by default
[    3.445530] clocksource: Switched to clocksource timer1
[    3.545892] NET: Registered protocol family 2
[    3.546622] TCP established hash table entries: 4096 (order: 2, 16384 
bytes)
[    3.546688] TCP bind hash table entries: 4096 (order: 4, 98304 bytes)
[    3.546824] TCP: Hash tables configured (established 4096 bind 4096)
[    3.546896] UDP hash table entries: 256 (order: 2, 16384 bytes)
[    3.546925] UDP-Lite hash table entries: 256 (order: 2, 16384 bytes)
[    3.547143] NET: Registered protocol family 1
[    3.547691] RPC: Registered named UNIX socket transport module.
[    3.547703] RPC: Registered udp transport module.
[    3.547710] RPC: Registered tcp transport module.
[    3.547717] RPC: Registered tcp NFSv4.1 backchannel transport module.
[    3.548242] Unpacking initramfs...
[    3.907597] Freeing initrd memory: 5320K (cface000 - d0000000)
[    3.908028] hw perfevents: enabled with armv7_cortex_a8 PMU driver, 5 
counters available
[    3.910297] futex hash table entries: 256 (order: 1, 8192 bytes)
[    3.910397] audit: initializing netlink subsys (disabled)
[    3.910468] audit: type=2000 audit(3.840:1): initialized
[    3.920259] zbud: loaded
[    3.920873] VFS: Disk quotas dquot_6.6.0
[    3.921099] VFS: Dquot-cache hash table entries: 1024 (order 0, 4096 
bytes)
[    3.923427] NFS: Registering the id_resolver key type
[    3.923490] Key type id_resolver registered
[    3.923499] Key type id_legacy registered
[    3.923522] nfs4filelayout_init: NFSv4 File Layout Driver Registering...
[    3.923817] fuse init (API version 7.23)
[    3.924357] SGI XFS with ACLs, security attributes, realtime, no debug 
enabled
[    3.932345] Block layer SCSI generic (bsg) driver version 0.4 loaded 
(major 249)
[    3.932550] io scheduler noop registered
[    3.932566] io scheduler deadline registered
[    3.932630] io scheduler cfq registered (default)
[    3.933663] pinctrl-single 44e10800.pinmux: 142 pins at pa f9e10800 size 
568
[    3.935444] Serial: 8250/16550 driver, 6 ports, IRQ sharing disabled
[    3.938330] 44e09000.serial: ttyS0 at MMIO 0x44e09000 (irq = 155, 
base_baud = 3000000) is a 8250
[    4.780792] console [ttyS0] enabled
[    4.785512] [drm] Initialized drm 1.1.0 20060810
[    4.791370] usbcore: registered new interface driver dln2
[    4.855562] davinci_mdio 4a101000.mdio: davinci mdio revision 1.6
[    4.861697] davinci_mdio 4a101000.mdio: detected phy mask fffffffe
[    4.868213] davinci_mdio: dt: updated phy_id[0] from phy_mask[fffffffe]
[    4.881250] libphy: 4a101000.mdio: probed
[    4.885304] davinci_mdio 4a101000.mdio: phy[0]: device 4a101000.mdio:00, 
driver SMSC LAN8710/LAN8720
[    4.895147] cpsw 4a100000.ethernet: Detected MACID = a0:f6:fd:8a:71:53
[    4.903327] ehci_hcd: USB 2.0 'Enhanced' Host Controller (EHCI) Driver
[    4.910012] ehci-platform: EHCI generic platform driver
[    4.915425] ehci-omap: OMAP-EHCI Host Controller driver
[    4.921022] usbcore: registered new interface driver usb-storage
[    4.928488] 47401300.usb-phy supply vcc not found, using dummy regulator
[    4.958888] 47401b00.usb-phy supply vcc not found, using dummy regulator
[    4.997710] musb-hdrc musb-hdrc.1.auto: MUSB HDRC host driver
[    5.003510] musb-hdrc musb-hdrc.1.auto: new USB bus registered, assigned 
bus number 1
[    5.011620] usb usb1: New USB device found, idVendor=1d6b, idProduct=0002
[    5.018443] usb usb1: New USB device strings: Mfr=3, Product=2, 
SerialNumber=1
[    5.025698] usb usb1: Product: MUSB HDRC host driver
[    5.030684] usb usb1: Manufacturer: Linux 4.4.16-bone-rt-r11 musb-hcd
[    5.037153] usb usb1: SerialNumber: musb-hdrc.1.auto
[    5.042875] hub 1-0:1.0: USB hub found
[    5.046681] hub 1-0:1.0: 1 port detected
[    5.084213] mousedev: PS/2 mouse device common for all mice
[    5.091665] omap_rtc 44e3e000.rtc: rtc core: registered 44e3e000.rtc as 
rtc0
[    5.099696] i2c /dev entries driver
[    5.103586] Driver for 1-wire Dallas network protocol.
[    5.110738] omap_wdt: OMAP Watchdog Timer Rev 0x01: initial timeout 60 
sec
[    5.118021] sdhci: Secure Digital Host Controller Interface driver
[    5.124231] sdhci: Copyright(c) Pierre Ossman
[    5.129011] omap_hsmmc 48060000.mmc: Got CD GPIO
[    5.205780] Synopsys Designware Multimedia Card Interface Driver
[    5.212038] sdhci-pltfm: SDHCI platform and OF driver helper
[    5.217864] hidraw: raw HID events driver (C) Jiri Kosina
[    5.223871] usbcore: registered new interface driver usbhid
[    5.229472] usbhid: USB HID core driver
[    5.233590] ashmem: initialized
[    5.237367]  remoteproc0: wkup_m3 is available
[    5.241838]  remoteproc0: Note: remoteproc is still under development 
and considered experimental.
[    5.243792] mmc0: host does not support reading read-only switch, 
assuming write-enable
[    5.246854] mmc0: new high speed SDHC card at address aaaa
[    5.255823] mmcblk0: mmc0:aaaa SL08G 7.40 GiB 
[    5.257386]  mmcblk0: p1
[    5.277184]  remoteproc0: THE BINARY FORMAT IS NOT YET FINALIZED, and 
backward compatibility isn't yet guaranteed.
[    5.290180] NET: Registered protocol family 10
[    5.295927] mip6: Mobile IPv6
[    5.298932] NET: Registered protocol family 17
[    5.303524] Key type dns_resolver registered
[    5.307822] mpls_gso: MPLS GSO support
[    5.311824] omap_voltage_late_init: Voltage driver support not added
[    5.318740] ThumbEE CPU extension supported.
[    5.323051] Registering SWP/SWPB emulation handler
[    5.328677] registered taskstats version 1
[    5.332950] zswap: loaded using pool lzo/zbud
[    5.339869] Btrfs loaded
[    5.361375] Key type encrypted registered
[    5.367645] input: tps65217_pwr_but as 
/devices/platform/ocp/44e0b000.i2c/i2c-0/0-0024/input/input0
[    5.403030] tps65217 0-0024: TPS65217 ID 0xe version 1.2
[    5.408865] at24 0-0050: 32768 byte 24c256 EEPROM, writable, 1 
bytes/write
[    5.415807] omap_i2c 44e0b000.i2c: bus 0 rev0.11 at 400 kHz
[    5.422873] at24 2-0054: 32768 byte 24c256 EEPROM, writable, 1 
bytes/write
[    5.430181] at24 2-0055: 32768 byte 24c256 EEPROM, writable, 1 
bytes/write
[    5.437423] at24 2-0056: 32768 byte 24c256 EEPROM, writable, 1 
bytes/write
[    5.444663] at24 2-0057: 32768 byte 24c256 EEPROM, writable, 1 
bytes/write
[    5.451593] omap_i2c 4819c000.i2c: bus 2 rev0.11 at 100 kHz
[    5.463657] bone_capemgr bone_capemgr: Baseboard: 
'A335BNLT,00C0,1216BBBK00A5'
[    5.470928] bone_capemgr bone_capemgr: 
compatible-baseboard=ti,beaglebone-black - #slots=4
[    5.535550] bone_capemgr bone_capemgr: slot #0: No cape found
[    5.595546] bone_capemgr bone_capemgr: slot #1: No cape found
[    5.655545] bone_capemgr bone_capemgr: slot #2: No cape found
[    5.715546] bone_capemgr bone_capemgr: slot #3: No cape found
[    5.721335] bone_capemgr bone_capemgr: enabled_partno PARTNO 'BB-APA-01' 
VER 'N/A' PR '0'
[    5.729549] bone_capemgr bone_capemgr: slot #4: override
[    5.734888] bone_capemgr bone_capemgr: Using override eeprom data at 
slot 4
[    5.741885] bone_capemgr bone_capemgr: slot #4: 'Override Board 
Name,00A0,Override Manuf,BB-APA-01'
[    5.751047] bone_capemgr bone_capemgr: enabled_partno PARTNO 'BB-ADC' 
VER 'N/A' PR '0'
[    5.759001] bone_capemgr bone_capemgr: slot #5: override
[    5.764337] bone_capemgr bone_capemgr: Using override eeprom data at 
slot 5
[    5.771333] bone_capemgr bone_capemgr: slot #5: 'Override Board 
Name,00A0,Override Manuf,BB-ADC'
[    5.780533] bone_capemgr bone_capemgr: initialized OK.
[    5.789203] 48024000.serial: ttyS2 at MMIO 0x48024000 (irq = 187, 
base_baud = 3000000) is a 8250
[    5.790279] bone_capemgr bone_capemgr: slot #5: dtbo 'BB-ADC-00A0.dtbo' 
loaded; overlay id #1
[    5.795844] 481a8000.serial: ttyS4 at MMIO 0x481a8000 (irq = 189, 
base_baud = 3000000) is a 8250
[    5.797143] 481aa000.serial: ttyS5 at MMIO 0x481aa000 (irq = 190, 
base_baud = 3000000) is a 8250
[    5.798317] 48022000.serial: ttyS1 at MMIO 0x48022000 (irq = 191, 
base_baud = 3000000) is a 8250
[    5.798702] bone_capemgr bone_capemgr: slot #4: dtbo 
'BB-APA-01-00A0.dtbo' loaded; overlay id #0
[    5.848485] omap_rtc 44e3e000.rtc: setting system clock to 2000-01-01 
00:00:01 UTC (946684801)
[    5.857171] of_cfs_init
[    5.859724] of_cfs_init: OK
[    5.868584] Freeing unused kernel memory: 472K (c0a94000 - c0b0a000)
Loading, please wait...
[    6.057862] systemd-udevd[117]: starting version 215
[    6.065012] random: systemd-udevd urandom read with 10 bits of entropy 
available
Begin: Loading essential drivers ... done.
Begin: Running /scripts/init-premount ... done.
Begin: Mounting root file system ... Begin: Running /scripts/local-top ... 
done.
Begin: Running /scripts/local-premount ... Scanning for Btrfs filesystems
done.
Begin: Will now check  file system ... fsck from util-linux 2.25.2
Checking all file systems.
done.
mount: can't find /root in /etc/fstab
done.
Target filesystem doesn't have requested 
/opt/scripts/tools/eMMC/init-eMMC-flasher-v3.sh.
Begin: Running /scripts/local-bottom ... done.
Begin: Running /scripts/init-bottom ... mount: mounting /dev on /root/dev 
failed: No such file or directory
done.
No init found. Try passing init= bootarg.
modprobe: module i8042 not found in modules.dep
modprobe: module ehci-pci not found in modules.dep
modprobe: module ehci-orion not found in modules.dep
modprobe: module uhci-hcd not found in modules.dep
modprobe: module ohci-hcd not found in modules.dep


BusyBox v1.22.1 (Debian 1:1.22.0-9+deb8u1) built-in shell (ash)
Enter 'help' for a list of built-in commands.

/bin/sh: can't access tty; job control turned off
(initramfs)

>
>

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