So I've somehow not noticed until now, but some default replacements mess up the alien visual override that give them the black eyes.

I'm fairly certain it's just the default replacement skins, but I'm not at all experienced with custom skins so I don't know what it is about them that's the problem.

Any ideas?

EDIT: I nearly forgot to mention, alien babies are also messed up. They have the voice, the game shows that they have 50% alien DNA, but as soon as the birth animation is over they return to being normal-skinned, normal-eyed babies.