Boy, I don't know. The only other two suggestions I have are both kind of extreme: (1) Upgrade to Ubuntu 6.10; and (2) try recompiling your kernel; maybe remove any kernel-throttling stuff, and make sure that the kernel is set with drivers for your CPU, motherboard, etc. But that's a long shot.
Hmm... You might just try double-checking that you're really using the nvidia driver and that you don't accidentally have something else running. Also, you might actually try using an OLDER version of the nvidia driver; you can get it from the same page, look for an archive link or something.
For the record, I'm using a Thinkpad G41 with a P4 3.2 GHz, NVIDIA Go5200 and 1.5 GB RAM, and I get a higher fps in Linux than in Windows. With my current settings I get about 60 fps in the Human base in Transit.
When I first switched over to Linux I thought my fps was slower because the game felt slower. It took me a while to realize the fps was actually faster, and I was just playing poorly.
