I had exactly the same problem with my old computer, which had the same GPU than yours, GF4 TI 4200 64 MB.
I could play the game very smooth (always around 50 FPS), but when facing a sun (tga-file) it always drops down to 50%, and then with later builds the "shivan thrusters" (the others strangly didn't seem to have that problem) done it finally, my FPS goes down beneath 10 as soon as I'm getting closer to lets say LOD1-distance (to give a rough distance-explanation) . Hull-damage particles made the same problem to me.
Not sure our engine-glows are from the media-vp, I rather doubt it. If you can , try another GPU if you have one laying around. I don't have this problem anymore, since I now have a new Computer. It may be worlds faster than my older, but at least there is absolutly no FPS-drop noticable by the parts mentioned above (now got a radeon 9800 pro).
Of course I don't suggest changing your hardware just because of this

, but maybe you have the possibilty to try it out.