However they seem to screw up the refresh rate with my monitor. I can't seem to set it to a non-flickery refresh rate, it seems to default to 60 hz or something no matter what I pick in the control panel. This includes the windows desktop as well as in the game itself.

This is "normal" for any quake3 engine based game. For some reason the Nvidia drivers and win 2000 don't get along, so the monitor jumps back to 60Hz.

To solve this I use a small util called Refreshlock. Pretty easy to work with and it does the trick.

One caveat : it also permits you to push your video signal way beyond your monitor spec. Beware of this.