Shouldn't really matter should it? They should work in both and if they don't it's driver error (the bug), not user error.
The major point of the control panel is having specific settings for specific games, using the global settings to force every game to use that settings is no use at all.
Thats why I stayed with the beta's that worked until the test patch and the in game AA/AF. I couldn't have my LFS settings when I was playing Crysis unless I liked playing at Etch-a-Sketch speeds and I didn't want to mess around with the global settings every time I wanted to play a different game.