I've had the exact same problem ever since I got Doom 3, and I have a FX 5900XT. I fixed it by rolling my drivers all the way back to 56.72.
I used to get FPS at around 60+, but whenever a certain texture or effect (often fire) would come on screen I would drop to about 15 FPS. It also...
Nvidia TNT 2 32MB
Nvidia GeForce 4 ti4200 64MB
Radeon 7000 Series 64MB
Nvidia MX440SE 64MB
Nvidia FX 5900XT
These are from 2 different computers. I used to have a 486 but I have no idea what was in that. I still have all these cards either laying around or in use.