This is a cut and paste from a gaming website with a guy discussing similar problems,, perhaps some things you can check into.
Do you have AA(Anti Aliasing) enabled in the game or the BIOS? It's very likely this is what is killing your performance (turn AA off!)
Also, what video mode are you on? Low/Medium/High/Ultra ? You should be on High, but not Ultra.
What version of drivers are you using? The 4.9 Catalysts(ATI you will need newest drivers for your card GEforce 6800 card) have big improvements over previous ones. However, if you are getting bad performance, maybe you have lingering files from old drivers. If you did not just clean format and install the Catalyst 4.9's (ie you have run a previous driver set before), then uninstall the 4.9 Catalysts, run Driver Cleaner and get rid of everything "ATI" and then reinstall the Catalysts 4.9's.
Have you tried increasing the "cachemegs" in the Doom3.cfg file to 128MB or 256MB (from the stock 32MB setting)?
What is your memory like before you open Doom3? Should be about 350-400MB free; hopefully nothing big is running in the background.
What is your 3dmark 2k3 score, and is it choppy in other games?
Is AGP 8X enabled in the BIOS?
I have worked on some of these issues on my PC as well as going to the AMD website and downloading the latest AGP drivers for my motherboard, might want to call AMD they are hard to get ahold of but a big help once you do...
One more thing. If you bought a BFGTECH card they have SPECIFIC drivers to help deal with specific problems. According to BFG the generic drivers get the card going but arent really tailored for any specific needs. Call their helpline and you should be able to get things straightened out. Those guys have been great so far. They asked me to call them back once AFPD comes in so they can help me optimize my settings to get the most out of this particular program. Might be worth a try for you.
Mike