My name is Neil and I am a cognitive psychologist. I use XFree86 with the NVidia driver and Mesa to program millisecond accuracy reaction time psychophysics experiments. I read this thread with some interest.
After upgrading to RH9 and installing 1.0-4363 my experiment programs were no longer able to update the screen every video frame, but instead only managed every other frame or every third. All of my hardware remained the same.
I eventually found that changing the colour depth from 24 to 16 bits in /etc/X11/XF86Config restored performance. I am not sure why this is the case, but I though it might be useful to you.
I am using:
nvidia.o Kernel Module 1.0-4363
Model: GeForce2 MX 100/200
Video BIOS: 03.11.01.26.00
Card Type: AGP
AGP Rate: 4x
Fast Writes: Disabled