I am playing Freecol and I can consistently reproduce a bug that causes the game to freeze.
Download the attached savegame.
Once loaded, select the Wagon Train in Vlissingen and press 'O' to make it execute its goto order. The city screen pops up, and now try to transfer the tobacco and the silver from the wagon train to the merchantman by draggin directly to the merchantman from the cargohold of the wagon train. This works, but now the game hangs, and I am unable to press the "Close" button.