I built a testmap to try out if it's a problem that only shows with certain models but it's really always like that. Normaly only parts of the same model don't get affected by the transparent material in front of them, but apparently the skytexture too.

I'm out of ideas now.
I will report this as a bug if nobody can tell me how to fix it. It's really annoying, especialy because it worked before.

so long...