lack of space dust
i didn't think any external setting will help, to bring back space dust

but i wouldn't be gernot if i didn't looked for the reason (or a possible one).
first i suspected the space dust might be produced by a field of vertices, cause when you open model 109 with "3d exploration" you can see a field of tiny polys or vertices (i suspect, cause only this prog. shows them). but after i checked the (text) output of ffe in theonis "frontier mesh viewer" i can say it's a ball array, so i tried to double the size of the ball_s for a first try...... (and erhm, theonis if you read this, 4000 (or 0040) is not 32768 only 64 or 128 if you double (why?), but i understand this backwards, f0rwards reading of data gets my head twisted too, the ball_s would be very big then, or maybe i'm wrong).
cowabunga

there they are back again (a bit fast and still very tiny).
i will post a altered .exe on ssc so you can check it out. i'm not shure why they are "filtered" out and if it's the program (distance or fog setting) or windows or grafx card, but i think they are simply to small to be seen.
i think further little tunings could be done, but i haven't the time to search and fix them all, personally i would like to see the targeting tunnels in ffed3d, i think it's a font issue (the tunnels are pruduced by the vector font i'm shure). but since ffed3d ports the strings of fe2 through a different codetable everything is mixed up, why they don't used the original fonts, even when the bitmap font is a bit crappy?
check if stardust's vanished even at the lowest possible res. ffed3d runs in

maybe this could be fixed too with ffed3d distance/tesselation setting, i'm not shure, any way this would make ffed3d only slower.