something is really wrong:
actions: 
1-removed /etc/apt/preferences
2-removed /var/lib/synaptic/preferences
3-sudo synaptic
4-lock/unlock version - not accepting this command at all  - no file 
"preferences"  appears in /etc/apt nor in "/var/lib/synaptic"

14:41:40 [EMAIL PROTECTED]:/var/lib/synaptic# ls -la
total 8
drwxr-xr-x  2 root root 4096 2006-10-23 14:28 .
drwxr-xr-x 68 root root 4096 2006-10-20 22:48 ..
14:41:42 [EMAIL PROTECTED]:/var/lib/synaptic# 

14:41:59 [EMAIL PROTECTED]:/etc/apt# ll
total 108
-rw-r--r-- 1 root root    40 2006-05-15 21:21 apt.conf
drwxr-xr-x 2 root root  4096 2006-10-20 14:04 apt.conf.d
-rw-r--r-- 1 root root   127 2006-05-15 21:21 apt.conf.org
-rw------- 1 root root     0 2006-05-15 18:41 secring.gpg
-rw-r--r-- 1 root root  1611 2006-10-20 18:34 sources.list
-rw-r--r-- 1 root root  3398 2006-10-14 07:19 sources.list~
-rw-r--r-- 1 root root  3063 2006-10-20 16:56 sources.list4
drwxr-xr-x 2 root root  4096 2006-04-18 22:47 sources.list.d
-rw-r--r-- 1 root root  2334 2006-10-20 13:33 sources.list.distUpgrade
-rw-r--r-- 1 root root  2098 2006-05-26 10:43 sources.list.org
-rw-r--r-- 1 root root  3256 2006-09-14 04:50 sources.list.org2
-rw-r--r-- 1 root root  3404 2006-10-14 07:06 sources.list.org3
-rw-r--r-- 1 root root  2344 2006-10-14 07:58 sources.list.save
-rw------- 1 root root  1200 2006-09-28 22:46 trustdb.gpg
-rw-r--r-- 1 root root 27681 2006-10-03 13:48 trusted.gpg
-rw-r--r-- 1 root root 27037 2006-09-28 22:46 trusted.gpg~
14:42:01 [EMAIL PROTECTED]:/etc/apt# 

5-while manually creating preferences it looks only in folder: 
/var/lib/synaptic as you said
6-no changes possible in preferences by means of gui->lock/unlock versions   - 
file preferences not changing at all
7-only manual changes in /var/lib/synaptic/preferences are visible in synaptic 

Let me know if more info needed

-- 
synaptic 0.58.7 and apt 0.6.45 don't follow pinned packages
https://launchpad.net/bugs/67398

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