With my installation on Vista, the files are located in the directory with the game program itself. However, I installed it in a different location (instead of 'Program Files', I use C:\Games\Larian...). I think the problem here (as far as the file locations are concerned) is that Vista virtualizes the 'Program Files' folder so that each user effectively has their own version of programs when they modify things. I believe the VirtualStore directories are where these user-specific changes are stored since they aren't technically allowed to modify the 'Program Files' folder.
On another note: I emailed a test savegame that is currently having problems.
-xalif
Ahh...That makes sense. Thanks for the clarification.