I have had a few ships not auto go into "Favored Ships" when i save them and they go in the huge list at the bottom under 'Speciality ships'.
It makes me think that they didnt save but once I look though that list they normally are their.
Also if you make a new ship and have to reload your save without making a new save, which i do sometimes If I miss move my ship or something, that also means the ship you made wont be available in your current save unless you start a new game due to how ship templates are saved. Likewise if you load a save you wont be able to see any new ships you have made in a different save/game as when you start a new game or save, the game makes copies of all the ship designs and adds them into the save file. There fore it cant see alternative save file ships.This is also the reason downloaded ships from the workshop only show up in a new game.
As for the naming convention, if you save it under a generic name does it work? i wonder if the hyphen at the end is effecting anything. Or I wonder if the name is to long that the game cant load the file even know when you save it can see that the file exists. I have had other games from other devs I have played in the past not pick up special characters when saving even know the file itself saves correctly. It should also be able to check if the file exists in the design folder. Documents\My Games\GalCiv3\Designs
Could any of those things be the cause ?