Hey there!
Thanks for sharing! yes the issue with the color scheme was related to minor races, trying to use the same scheme. I've had to create additional color schemes that are not very creative (some lights change/etc.) to stop running into issues. GRM Militia now for example, has a sister, GRM Tribal, where the brown is made lighter, and the engine color is green instead of red/orange.
However, I WAS STILL running into this problem. What fixed it? I had been using two races with the same map color. This was conflicting and for some reason when the map color got changed, so too, did the ship appearance. Fixed the map color, and appearances showed up correctly. So weird.
Also thank you for the kind words, and I'll not speculate on how "troggleballs" came up bro. What you are using the mod for, is exactly what I intended, so that you could create YOUR universe. My ships just help 
I LOVELOVELOVE constructive feedback! I didn't quite see the point in the strengths and weaknesses sections, so I generally just filled them to fill them.
Perhaps the explanation of the race in general, should go there, and the top part, be a little vignette from the race's perspective?