Selecting All features on, I seem to get White ships (frigate class I think) the only mission I've seen this on is The Romans Blunder.
Whilst the ship you chase, the "Icarus" is normal, the ships that come after are white until they are destroyed, but the fighters they launch aren't white.
Going back to standard freespace 2 settings stops this happening.

Well, easiest fix is not to set everything on. It's a texture problem of some sort, I'm assuming they're showing up white with black lines? That's what they look like when you don't have a texture or can't properly render them. There have been some issues reported with certain video cards in the past (If I remember correctly certain Geforce drivers), so it could be due to that...