I was having problems being able to overwrite saved games so I looked through this forum and someone advised to run the program as an administrator. Well that worked, autosave worked again and I could overwrite save games. Unfortunately all of my old saves disappeared.

If I stop running the game as an admin they come back but I'm no longer able to overwrite saves. I haven't gotten far in this game, maybe an hour and a half of play time before I noticed I had an issue, but I'd prefer not to replay the areas I've already gone through.

May depend on the system, but on Win 7 64b it's:
C:\Users\Admin\AppData\Local\VirtualStore\

The AppData folder is hidden by default, you have to go into folder options and make hidden files and folders visible. This is assuming you have Vista or Win7, there's no such folder in XP.

Thank you, the problem is solved. Luckily I had Arcanum to distract me away from just starting over again.