I have heard of this one as well. I believe that the actual human skull is the skull in the headboard of the bed in the beginning of the ride. Now, this is not fact of course, merely a rumor. Although, the story goes that when Pirates of the Caribbean was being built, artificial skulls were not life like enough for Disney. So, they simply used real human skulls. After technology progressed, they went through and replaced the human skulls with artificial skulls. However, to remove the skull in the headboard of the bed would require the entire headboard to be removed. So, the Imagineers just left it there. Like I stated, this is simply a rumor, but it is a pretty interesting story!