You didn't mention whether this was DA or TA, but I used to have that problem with older versions of Twilight. If you are talking about TA, have you updated to 2.03?
BTW, the game loads the ship files only when you start a new one. Once the game has been created, it no longer reads them. So, any ships you want in the game need to be in the ships directory beforehand. I actually save the ships files off then restore them prior to a new game. Also, deleting a ship in the game deletes the associated files.