Window Position & Prefs "Gone"

Every time I start up or restart, any window position, size, view etc info is gone, and I get a view very different than what I had set. I have tried to delete the Finder plist, but it did not help. I did notice something extremely weird as well.
I noticed that the Finder plist is actually deleting itself about every 30 - 60 seconds when I open the ~user Library prefs, and cannot find anything that might be causing this. Repairing permissions, running utilities such as DiskWarrior etc have not helped. This condition actually exists identically on two Macs I am using. The only thing in common is that I ran an updater for Missing Sync for BlackBerry from Mark/Space Software, and took note of the condition being created on the second Mac immediately after doing this update.
I don't really want to do a full reinstall of the System, as I suspect I will still end up with this "condition" after reinstalling my working applications.
Any suggestions would be appreciated.

A bit of troubleshooting .....
On a full restart, any windows left open will retain their position, view, etc - but closed windows "forget" when reopened.
During the safe boots, files were sent to the Trash, which are as follows:
In a folder called 501.245359984
and a folder called 501.245361007
annex_aux
annex.db
filetoken.db
FondResourceCache (only in the first folder above)
fonts.db
Local.fcache
qdfams.db
System.fcache
User.fcache
My startup items under my account are
iTunesHelper
Microsoft AU Daemon
iKey
MicrosoftMouseHelper
MicrosoftKeyboardHelper
Dashboard KickStart
EEventManager
iCalAlarmScheduler
textsoapHelper
Epson Scanner Monitor
All of these items were already in place - for a long time - before this problem started.
I cannot find /private in order to locate /private/var/run/StartupItems
Nothing unusual (at least that I can see) in either of the other two locations.

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