Is the external drive a unit you've bought completely as-is (like a WD Mybook), or did you buy the 3TB drive separately and put it in an old external enclosure yourself?
I had this also happen to me, in a case where the old external enclosure didn't function well with more recent, big drives. You can get the strangest results that way. That may be a reason. Maybe the enclosure's chipset doesn't get along with GPT formatting or something.

Otherwise, maybe a dodgy cable?