So, got a tiny problem with the ship designer. The one that you choose from the main menu.
See below, I have picked a custom set of colours for my civ's ships. (Sorry, if the screenshot is huge)
When I go to the ship designer, I can't pick my custom civ's ship colours from a menu. I can only pick the defaults.
The problem with this, is, if I design a new ship in the main menu Ship Designer, it's not going to use my custom civ's ship palette. This means that I'm not going to know what it really looks like until I'm playing a game.