How is D3D looking on your rig? I always got those artifacts from Hellfire motor smoke that would cut up my 2D cockpit. Plus other minor gripes such as the canopy glass having a shiny mirror-look in external view. I also think the game runs faster by default in D3D, as it can make full use of the power of your graphics card, unhindered. When running 3DFX through a glide wrapper, you can turn on VSync to slow things down a bit and essentially limit the framerate.

If you haven't seen it already, take a look at my Display Mode Comparison page: