You talking about ATi tray tools or ATi Tool?
I've never had problems with ATi Tray Tools and it's perfect for Oblivion because you can set up profiles so that when you load up Oblivion it automatically sets your desired AA/AF levels, then returns them back to normal when you exit the game.
If ATT does indeed cause problems with certain games, then you can just set AA/AF manually and just close ATT down before starting the game. ATT doesn't have to be running all the time for AA/AF settings to take effect.