One issue that hasn't been touched yet and which I discovered semi-accidentally.
If you have any extreme values in either red or green channel, they will "burn through" in FS2_Open, creating nasty nasty black flecks to appear on the surface of the ship.
What this means is that you will need to look out for overcontrasting the image, since if red or green channel values are either zero or 255, black flecks will appear. If you meet this issue, simply reduce the contrast by a low amount like three or five units.
For example, colour [0,255,128] (#00ff08) will result in black flecks, while colour [2,253,128] (#01fe08) will not.