I don't think it will help, but before submitting a bug report to Stardock, try to "verify the integrity of game cache" from Steam. Maybe something got bugged. I usually don't create my own ships, I use models from Steam Workshop, so I can't really help you there, I don't even know what these parts look like...
If the refresh doesn't work (and restarting Steam also), submit a bug report to Stardock:
https://esupport.stardock.com/index.php?/Default/Tickets/Submit/Index
include a save game, your debug.err file, you prefs.ini files found \My documents\My games\Galciv3
someone from Stardock will answer you on Monday, or someone else here will see this thread a be able to help you.