My friend has a Radeon 9800 Pro and has this problem, I dunno what it's called, it sounds familiar. This is how he described it:

the main problem is flickering green and blue boxes all over the textures. Also, the lightsaber appears to have a greenish flickering rectangle around it. I can also view the invisible walls at the end of FFA_Bespin, something I shouldn't be seeing (the wall I see is in the from of the flickering green and blue boxes). Anything you can do to help me out would be greatly appreciated, since I'm quite eager to play JK2 again flickering box-free.

Green and Blue boxes. If you'd like, I could find a way to get a Screenie up here. If know one knows how to solve this problem, at least help figure out the name of this particular problem. OpenGL? I dunno.

After patching to the latest official version I'd suggest updating his video card drivers. I don't know what the specific bug is called, but you can have him look in his console and scroll up to see any error messages. Then do a "condump" (like: condump errors) to make a text file in his base with the text saved to refer to later.