I have had this happen to me twice today.
I have a fresh version of OS 10.7.4 that was installed on a zereoed out hard drive before installation. All system updates applied.
Local User Account named "Profile User". I configure the account as I would like, changed desktop, dock, etc. After a few logins, then back out. Everything will seem fine, then out of nowhere I will log in to the account and EVERYTHING has reverted back to 'factory settings' as if I had just created a brand new user account. This User's Library Folder (hidden), will be completely overwritten with defaults (from /System/Library/User Templates/English.proj) or so it seems.
As I'm trying to set up a default profile for a lab configuration, this is getting very frustrating, as I'm having to do work over and over and over again.
Anyone have any insight on this or seen similar behavior??