Sounds like some sort of utility that runs on the mac when you start up is deleting the preference files.
That happens to Windows users who ru the paranois settings on TweakUI, but I have no idea if there's anything like that out ther for Macs.
You should make a backup set of good ones, though, so you can just copy them in until you get it straightened out, or use a startup script or Blatner Tools to set the prefs every time ID starts.
Even after making a copy of the preference file and replacing the default one with the copied one, it still reverted back to the program default one after he booted up the iMac from being shut down the night before.
I did however, find a free preference startup script from: http://in-tools.com/article/scripts-blog/preference-manager-script
This fix worked for him. The only thing this script can't set are Print or Work Space preferences, but you can save those seperately.
Thanks for the tips.
I didn't mean a backup set of prefs would prevent the reset, jus that after a reboot you could copy them back so the user wouldn't need to reset each one manually.