actually its probably verticle sync in the drivers. Your framerate is being capped by your resolution/refresh rate. If you go into your drivers settings you should be able to disable verticle sync. I also think there might be a way to tell quake 3 to ignore verticle sync and render the highest FPS possible, but I don't know many quake 3 console commands so I'm not sure what it is.
If my response is brief and vague its because the info you provided is too!