It would be the same problem though (incorrect image files). Make sure no other mods are providing bad data and that you don't have any extra effect files in there which might be causing the problem. You can pretty much only get those black squares if the effect is DXT5 or 32-bit TGA when it should be DXT1 or 24-bit TGA (ie, images that shouldn't have an alpha layer). ANI, PCX and JPG images can't get rendered wrong like that since ANI is at most 24-bit (if using -img2dds), PCX is ignored completely, and JPG can only be 24-bit.
I think there might be more to it than that - it seems that only the bitmap in the "@Laser Glow:" field is rendered for primary weapon types ATM.
Anything I try in the "@Laser Bitmap:" field shows up as a black square in game as far as I can tell. Images without an alpha channel seem to have their black square backgrounds showing, such as the flak shots, and I don't think "@Laser Glow:" bitmap glows escape this totally either.
A few missile trails still have black background outlines, and some beams or pieces of beams are now missing. :\
Also, non-flak muzzleflashes don't appear to display when firing out of turrets anymore either - though if you arm the weapon on yourself, they do appear.
None of the above was present before the RC2 release - "fs2_open_T-20060513.exe".
Errm, should I mantis this or does it sound more like a messy install? Is anyone else having similar issues?
Other than that though, this build's rock solid. Not a crash in sight. Awesome work.