Should have thought of this before, but if you have Windows Vista and installed the game to the default Program Files folder path, and depending on how you have your user accounts set up, Vista can create the savegames folder under the user data folder, and map that folder to where the game expects it to be when the game is started. Perhaps it did the same with the config.div file? Check for the file in the location;
C:\Users\{account name}\AppData\Local\VirtualStore\Program Files\Divine Divinity\Run\config.div
