I run all my games using only the latest ATI driver and in-game settings. I have not had an issue for 3 or 4 years. Thing is, I do not play all the games -- so, that does not mean there are no problems to be had.
I've read articles that indicate most developers put all the "safe" video options in their in-game options page. If they leave something out of their own settings, its for a reason. AA is often left out. So, since I like how the games look using the in-game settings, I never feel like I have to use the Catalyst Control Center to over-ride in-game settings.
Still, some people like to do that a lot. I think because most games are developed on Nvidia hardware via TWIMTBP, Nvidia users have fewer issues overall when using a "control panel" to override the in-game settings. I think, in general, neither Nvidia nor ATI promise one can override every setting of every game and have it work. Also, it may work and be broken when a new driver arrives.
Anyhow, as RSC indicates, eliminate CCC overrides. That may help. To be sure they are eliminated, one could uninstall the CCC including any settings files -- while leaving the driver in place. If that worked, reinstall CCC.
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