Take a look into the /data/fs2_open.log
A few lines under this[...]
Initializing OpenGL graphics device at 1024x768 with 32-bit color...
Initializing WGL...
Requested WGL Video values = R: 8, G: 8, B: 8, depth: 32, double-buffer: 1
Actual WGL Video values = R: 8, G: 8, B: 8, depth: 32, double-buffer: 1
OpenGL Vendor : NVIDIA Corporation
OpenGL Renderer : GeForce 8800 GT/PCI/SSE2
OpenGL Version : 2.1.2
[...], you can see if the shaders compiled on your card.
Compiling shader->
Also check your OpenGL version.
The Radeon 9800 won't work with the shaders, as shader model 3.0 is the minimum required for the standard shaders.