I have pretty much the same problem - recently my computer stopped loading, saying C:\windows\system32\config\system was non existant or corrupt. Following advice from dell, my computer provider I replaced the files system, security, sam, software and default in that folder. now my computer is working OK, but I've lost loads of settings in windows, and I'm having the same problem with my office applications. I have noticed the appearence of a folder 'Owner.DC6HZ31J' in c:\documents and settings. This has only just appeared, and I definitely did not put it there. I also found that the registered user on my computer was set to 'Preferred User', and the computer name had reverted to what it was originally.
I presume certain settings - user names, company name etc. were included in the files I needed to replace, but beyond that I have no idea how to sort it out.