Hmm, I run it with normal FPS on a GeForce 6600, NVidia 185 driver. Can you try to disable the extensions r_ext_vertex_shader, r_ext_vertex_buffer_object and r_ext_occlusion_query to find out if it is related to one of them ?
A few graphical glitches are related to color clipping, the q3 engine has to compute colors on the CPU and pass them via OpenGL to the GPU, so they are automatically clipped to [0,1]. When I generate the colors in a shader program, they are not clipped, so color values above 1 or below 0 are possible, you can see this on the booster. The booster shader has a sin rgbGen that goes between -1 and 1, but in the normal game it is clamped at 0, while in the GLSL code it is not, so the color gets darker than normal.
The clipping bug is strange, it looks as if there are some refEntites not rendered.