I was going to put this issue to bed, but I accidentally stumbled upon something very interesting. You see, I was going to write everything off as a possible linux kernel issue. Just to sate my curiosity however, I decided to install the linux version of Quake 4 and benchmark it as well. Since it's based off of the Doom 3 engine, I expected the scores to be abysmal, right? Wrong! Here were my Quake 4 settings when I noticed something was up...
1280x1024, High Quality, 2x AA, SMP enabled --> 61.71 fps
Seeing that, I was a bit shocked. Those same settings under Doom 3 (minus SMP) gave me 55.2 fps. That's right. Quake 4 was outperforming the supposedly less intensive Doom 3. Here are the side by side scores for Quake 4 on Windows vs. Linux.
Windows, 1280x1024, High Quality, 4x AA, SMP --> 57.77 fps
Linux, 1280x1024, High Quality, 4x AA, SMP ------> 56.66 fps
THAT is the kind of performance that I'm used to seeing. Linux being within one or two fps of windows performance. To further test my theory, I did a slight overclock on my 7900 GS. 510 core/700 memory. Doom 3 performance DROPPED from 55.2 fps with 2x AA to 53.8 fps! Predictably, Quake 4 performance went up to 57.20 fps with 4x AA. These two programs are really the only things I have to benchmark linux performance, but it is apparent now that there is an issue there with Doom 3. I'm not certain if it's just the linux version of Doom 3 not working well with my motherboard or if it's the nvidia drivers. Personally, I'd bet on Doom 3 being buggered up.
Sorry to bother you with all of my troubles netllama, but I'm happy knowing that my 7900 GS is performing up to specs after all. Guess I'm down to just one reliable 3d benchmark in linux now, but that's not so bad I guess. Thanks for your help. Take care.