I have the exact same problem. What I have found is that it happens on some games(doom3 nwn or anything using cedega) and others work fine(q3a et glxgears). The solution Ive figured out for this is to run glxgears before running the game. This enables me to play any game just fine. If I go from one game right to the other my system does lock. I have to let it sit for awhile before I can switch games. The reason for this is that the card screws up switching from 2D mode to semi-3D mode. This is best explained here.
Ive also read that some windows users are seeing this problem.
My system specs:
OS: Gentoo Linux 2005.0 x86_64
CPU: AMD64 3500+
Video Card: eVGA nVidia FX 5900 Ultra
Mother Board: ASUS A8V Delux