I have just tried a couple ship boarding events and I do not experience this myself.
Does this happen every time you board a ship?
If not, do you still have the boarding save for this instance, and if you reload that save, does it happen every time?
If either of the questions is "yes", can you send me your save, and also inside the SAVE folder there are folders for each profile you are using for the game, there should also be an "options" folder inside the profile you are using; please send the contents of that folder too. You can zip the save game and the options folder together.
Email to chezjfrey@hotmail.com