Ha, I haven't used ATI's CCC since forever so I can't be sure on the following.
Even if you use CCC you can save profiles for each & every game or application title. The option to do this 'should' be in the colour management settings, either directly through CCC or by way of the desktop properties, Settings > Advanced. Basically, all you should have to do is adjust your settings as required, Save Profile As and it will retain the current display calibration you have applied. Change & tweak for other titles and save as again......
I suspect what you are describing is the CCC's 'Smart Detect' (or something close to that) where it can tell whether your are running a full screen 3d app or just using the desktop, in this instance itonlyhas 2 profile settings.
Try accessing the settings through the display properties. Right Click on Desktop > Properties > Settings > Advanced and see if you can apply profiles that way.
Failing that mate, wait for someone using the latest CCC to help.
