Berthing a ship is not normally a problem. Berthing a ship so that you don't have a ship at all, just before the quest is about to give you a new ship, may cause trouble, and that's what we're trying to fix.
You don't get the Santiago at the start, you get it some way into the story when you capture the pirate Charles Baxter. You do that at Charlestown on Nevis. Did you berth a ship there before you captured him and got the Santiago?
In any case, hopefully this will provide a quick fix for your game. Download the file, copy it into your "PROGRAM" folder, load your game and press F12. You should see a message on screen, "Executed Console". After that, you should be able to sell a ship without crashing the game.
You don't get the Santiago at the start, you get it some way into the story when you capture the pirate Charles Baxter. You do that at Charlestown on Nevis. Did you berth a ship there before you captured him and got the Santiago?
In any case, hopefully this will provide a quick fix for your game. Download the file, copy it into your "PROGRAM" folder, load your game and press F12. You should see a message on screen, "Executed Console". After that, you should be able to sell a ship without crashing the game.