Oh, and I almost forgot, here's one I noticed almost immediately back at launch (version 1.0!), and it still isn't fixed now over 2 years later, rofl...
The *second* Material selector in the Appearance tab of the CivBuilder, is always on "Material 1" when you first enter the screen, regardless of what value is specified by the race/faction you're working on. It does USE the real value to shade the big 3D model on the right, but unless you already know what it is, good luck figuring it out from the selector lol.
I've never actually bothered to complain about this because I switched over to defining all my custom races in XML a loooong time ago, so I don't need to care. But I'm surprised it's still never come up here on the forum, to the best of my knowledge. 