In Windows XP, set the compatibility mode to Windows 98 / ME and make sure it runs in 640x480 initially. Then in the game, set your screen size.
To do this:
1. Right click quake3.exe in winxp and goto properties.
2. Click Compatibility Tab.
3. Tick first box and select win 98 / ME compatibility mode.
4. Tick the box beside the 640x480 text.