Oh, re-install; that should not be necessary. If you did have to, the un-install program asks you if you would like to keep the saved games and settings, and you can copy/zip all of the folders in the '..\Divine Divinity\Run\savegames' folder to back them up.
From the readme file;
Problem: Black squares appear around the imagery in the game
Cause: Your video card does not support color keying.
Solution: Turn on the alpha bit in the configuration tool.
