I just had a thought after reading some of the blog posts on here. I apologise in advance if it's been said before, but I was thinking about the season 3 episode, "The Man Behind The Curtain," and the revelation of "Jacob" in the rocking chair. For me, I'm pretty sure that wasn't Jacob, more likely MIB. But since then, we've seen MIB, in Locke form and Titus Welliver form, and he looks nothing like the guy in the chair. We know MIB can take on the forms of the deceased, so maybes at that point he was taking on the form of someone we have not seen yet - I was thinking possibly the captain of the Black Rock, Magnus Hanso? I assume he died on the island, in unknown circumstances, he may have had connections with MIB on the island. I do hope we see more of the Black Rock after watching Dr. Linus, which was awesome by the way.
Just a theory from my humble little mind, would love to hear your thoughts :)