Ahhhh, I know what's wrong with that!
It's fucked.
Sounds like your driver installation is not too healthy. The fx5500 wasn't a
great card, but it was fine for basic OpenGL and would have been able to run Q3A OK. Updating your drivers might be all you need:
http://www.nvidia.com/object/winvista_x86_96.85_2.html (32-bit)
http://www.nvidia.com/object/winvista_x64_96.85_2.html (64-bit).
Another alternative would be to try out the D3D8 wrapper I have available here:
http://quakeone.com/mh
This can be implemented in GLQuake right now with a minimum of fuss, takes maybe 5 minutes work to do, and will give instant results. Look at the "DirectFitz" engine for the most up-to-date version and a sample working implementation.
It's not a complete OpenGL implementation, being limited to the calls that the various Quake engines it's been implemented on use. But it's better than nothing.
You'll also need a DirectX 8 SDK for it, which unfortunately Microsoft don't publish any more. A quick look around on Google will get you a copy of it.
A third option might be something like this:
http://shop.ebay.com/i.html?_nkw=geforc ... m270.l1313
We're literally talking beer money prices (less than $5 in one case!) and it will completely obliterate the 5500.