I read a lot about this behavior in Google searches and have even posted here about this before. But now I'm back armed with more experience with the problem.
We have a Win 2003 domain with some 2008 member servers. (AD is 2003 functional level.) Over the past year I've been updating our computers to Windows 7. All workstations are 32-bit 7 Enterprise. I don't use WDS to deploy an OS, it's all from scratch the old fashioned way.
During initial setup I configure our admin profile on each computer with a few basic settings. Black wallpaper (to differentiate from a user account), customize the system tray to always show a few icons, etc.
If I periodically go back to a computer the account is fine. However, if I haven't logged in with the admin account on a computer in some months Windows will see fit to re-build a brand new profile. This is confirmed by the user profile being the admin user account with .DOMAIN appended. In some cases I've had it happen a second time, adminuser.DOMAIN.000.
I figured this was only happening to the admin account and was harmless. Now it has happened to a user that is on the computer most of every workday. This does not appear related to power outages or Windows Updates. The computer's names haven't been changed. No domain changes or OU moves. This particular problem never, ever happened with Windows XP. AD and GPO changes are extremely rare for us.
I know the accepted resolution is to just grab the contents of the old profile and move it to the new profile but, really, this simply shouldn't be happening. Anyone have any ideas for causes?