I'm getting the exact same problem as this guy on the same exact version of the game. He never got an answer but I assume it's because he posted it on the wrong forum.
So anyway, got the ultimate edition on Steam and everytime I see a custom ship on the map or in battle it looks like the guns and stuff were randomly placed on the ship. With additional wings or other parts stacked ontop of each other where they don't belong.
Looks fine in the ship builder but looks terrible on the map and in battles.
For such a big feature of the game... it's kinda pointless spending hours meticulously creating new ships when they end up being a disorganized mess.
Edit: Oh I forgot to add that I also launched the game from different exe's in the past. Since there's no launcher or anything that lets you select what you want to play for the steam version.