Quick Question E01, did you ever follow the sage advice of Uninstalling FO3 and reinstalling? I can't remember if you said you did or not.
By that I mean, uninstalling with the uninstaller, nuking everything in Data and My Games/Fallout 3, and reinstalling free and clear.
Uninstalled, did a defrag, then decided to reinstall windows

Did a complete format of the drive, reinstalled windows, then installed GOTY editon...so yeah...I'd call that a 'reinstall' lol!