You can probably do it using the command line, I remember this issue all too well. It always crept up if I used the Voodoo settings option in Quake 3. I remember that I used to uninstall and reinstall the game and just avoid that option and would run perfectly on any other card I had attached.

/r_glDriver opengl32

alternatively you can toss this into your shortcut:

quake3.exe +set r_glDriver opengl32

The reason why Q3 starts Voodoo first is the assumption of "oh, since you have a v2 you must have a really shitty host video card, so let's start v2 for your sake"

Alternatively you can set r_maskMinidriver to 0.

Great, that worked like a charm...well almost. As soon as i changed resolution it went back to the voodoo card.
The solution for that was to set the resolution manually from inside the q3config.cfg.

Jumped from 39 to 78 fps on demo four with everything at hight at 800x600!