I've had this problem since Debian Squeeze, I've upgraded to sid to get all of the updates to get rid of a bug that severely hurts gameplay in TF2. I've even tried to switch from Auto to Manual mode for the nvidia module.
My specs:sudo update-alternatives --config glx
There are 2 choices for the alternative glx (providing /usr/lib/glx).
Selection Path Priority Status
------------------------------------------------------------
0 /usr/lib/nvidia 100 auto mode
1 /usr/lib/mesa-diverted 5 manual mode
* 2 /usr/lib/nvidia 100 manual mode
Press enter to keep the current choice[*], or type selection number:
Core 2 Quad 2.4GHz; stock speed
3GB DDR2 RAM
Nvidia GeForce 9800GT
Any help would be appreciated.