Sorry to Necro thread and all... but this is the ONLY post that describes exactly what I have just encountered.
I have a custom alien that looks GREAT, and still does. I even have him saved so I can copy his species. However, when I create a new alien and load the species up, the base complexion is reset and when I put it back to Neck Scales, it looks VERY different, as per the OP. This also occurs when I have the original character go to the tailor.
What happened? >.>
I want to share this species with a friend, but the look is so different that I am not so sure anymore.
P.S. I just came back from like a year of being away.