It's as Pieter said: lack of icon variety to differentiate much between those ships.Meanwhile the Revenge and Golden Hind both share the same icon as the big Spanish galleons, and if those all count as the same broad ship type then we may as well just have one icon for everything because about the only thing those three ships have in common is that they are in fact sailing ships.
You'd be welcome to do another pass on all ships to see which ones could do with having different icons reassigned.
Now would be a good time for it, if you're considering adding more icons anyway.
Perhaps it's worth combining ships_1 and ships_2 into a new or expanded texture, as well? They're only separate because that's how they were in the original game (ships_2 was for the Black Pearl and Fearless models).
Also, make sure the shipsTR file is exported with the same high quality settings as the other three, otherwise it will look noticeably different.