It's something to do with OpenGL. Those games you mentioned are all Direct3D.
It's a Quake 4 engine-specific bug. Prey was one of the first games I loaded up when I installed my 8800GT, and was puzzled at my constant 20FPS in it at the same settingss as I had on my 7900GT. Then remembered this irritating bug.
Nvidia just needs to set the single-display performance option for these games in their drivers, they already have default profiles for the games affected in the driver package already, pretty simple way to keep their users from having undue headaches.
I got this free with my new vidcard, but haven't really played it yet. I need to start, since I actually loved the beta. None of my buddies picked up the game though