There should be a link in the Start menu folder for DD to run the configuration program again, or you could browse to the file in Windows Explorer (..\Divine Divinity\Run\configtool.exe) to start it or make your own shortcut.
At least with the disk version you can change the resolution manually by editing the '..\Divine Divinity\Run\config.div' file in a text editor. The same can probably be done in the download version.

The desktop composition option is more for graphics and compatibility problems. I didn't have high hopes it would help for performance issues, but it was worth a shot.

How did you lose your saves? Some people have had problems trying to load saves made in the disk version with the download version of the game.
If your saves just disappeared, Windows may have just changed where the game was looking for them. Under Vista/7, depending on how the user accounts are set up, if you install the game to the default Program Files path, Windows can create separate savegame folders for each user, and then map that folder to the game's savegame folder (so it will just see the saves for the relevant user).
C:\Users\ %account name% \AppData\Local\VirtualStore\Program Files\Divine Divinity\Run\savegames