i had the same problem, but i figured out a work around! as soon as you enter the ship tailor, hit the randomize button, after that the colors will work again and you can just fix your ship the way you want it in the advanced section!
Whoa, seriously? Guess what I'm trying the next time I log on.
Randomize workaround confirmed. I was able to do it on my Fleet Dhael with the vet skin. After hitting randomize a few times I was able to use the paint patterns and have them show up properly with no problems. I can grab pics later if anyone wants them.
its the costume engine thats broken, not the costume.
let me explain:
whenever you sart e customization, on many materials nothing will change when you change sth.
now try to first click on one of the standardized variants on the left. this will reset the engine, and whoops, now customization works as intended.
second way is: start customization, cancel it, start it again, will work too.
somehow the engine is broken in that part. its definetely not the costume-variant itself. though on the "special" materials or materials linked with shield-atered skins this problem occurs more often.