I had such problem. My solution for it: go to "//my documents/my games/GalCiv3/" and delete '/design' directory from there. Unfortunately in that directory saved all your custom ship designs, so you should copy it somewhere else and only after delete it. Lately you may return at last part of your ships back in game, but don't be greedy, and take back only designs you really need. Also try not to copy back designs you recieve from multiplayer, I think, that whole trouble is in there.

Well... some update to my advice: I just have such problem once more, and started looking throw 'designs' for mistakes, and found one, that i think will be a solution to the problem- in designs i found files belong to... nothing (picture was completely black), I deleted that files and everithin go to work correctly.

Derek, I`ve sent my rough files to you. Hope devs could fix that problem.