Yeah, I think swapping the order was a really bad move that damaged both episodes: this one because it beggars belief that Amy and Rory don't react at all to the father-and-son drama, and the pirates episode because it ended up looking shoddily written/edited when it shouldn't have (admittedly this is just conjecture but I can't believe nobody noticed the pirate vanishing from the story despite being in a locked room with the main characters - so I'm guessing there was a scene about Melody that got pulled).