I have After Effects CS6 in a computer where also CS5.5 is installed. 64bit windows 7 Ultimate 20GB memory and two AMD Radeon HD 6900 Series Display adapters with drivers updated an hour ago (Driver date 27.7.2012, version 8.982.0.0).
When trying to use After Ecffects, I get error message "After Effect warning: A problem occurred when processing OpenGL commands" immediately when clicking Composition window.
What could be done?
Not much, I'm afraid. You probably need an older graphics driver. Other than that you could always disable the second card or play with the configuration. Unfortunately some not so smart person decided that CS6 would no longer need manual OpenGL control for the user, so there's no way to suppress it from within the program to force-revert to software-only modes in case of such issues...