This is a fairly common bug, unfortunately. The only thing I can suggest is patching your game. I had this bug once, but in was with the "Sunrise/Sunset" movies in BG city. I only had the problem in that one game, and my method of solving it was to simply not be outdoors at dawn or dusk. Unhappily, a solution that simple won't work in this case.
Perhaps you might be able to go into the Baldur.ini file and see which movies have already been played, and turn on the flag for the "Entering Balduran's Ship" movie, so your game won't try to play it.
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Volothamp's Comeuppance
Everything you ever needed to know about the entire Baldur's Gate series......except spoilers.
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