Might be simpler to organize the shipsets manually... you just need to put files named ship1.bmp, ship2.bmp, ship3.bmp, etc. (png works too) in your graphics folder; these will override the default ships in ships.bm2. Black is the color of transparency, i'm guessing the shipset organizer adds it to make different ships of different sizes fit in the same image. But as of Continuum .37 I think, you can override single ships with the method described above, which makes the organizer pretty much obsolete. (I never used it, but it sounds like it's what it does.) If the black square is visible ingame, then it's "non-pure" black (not exactly RGB(0,0,0)), and you could always try changing the color depth in your options. As for the roll, I'm not sure if it can work with custom ship graphics... otherwise you'd get a standard warbird roll in a zone where they put a custom warbird. So it would change appearance ingame. Notice the files wbroll, jvroll, sproll, lvroll, weroll, nwroll (that's the lanc), and shroll. I'm not exactly sure what you need to do to use a custom roll...