I'm encountering a problem with using the Omega Star Trek ship design pack in my game. Omega mod is loaded, and ship designs appear as normal in my shipyard screen, but when I try to modify the designs and then save them under a different name, the game tells me that I cannot modify a core ship design.

After reading the OmegaMod author's comments in the library of the galciv website, I moved the model files over to the Mods folder, played a game, and was able to upgrade and save. However, after starting another game, the problem has returned. Why does the game think these are core ship designs, and how do I convince it otherwise?