I don't think this happened to anyone before. Are you sure you picked up the skull and not dropped it somewhere?
If you can't find the skull, you'll have to reload a game. (You do have a save from before you've came to the island, no?

)
Or, if you want to, you can send me a save (on the island) and I'll add the skull to your inventory. (See:
viewtopic.php?f=3&t=4624)