This thought just crossed my mind. In The Incident Jacob said that "it only ends once. Everything before that is just progress."
Now after Jacob was stabbed he fell into the fire and turned to ash. Pheonixes are supernatural beings that burn up and are born again from their ashes. What if that's what happens to Jacob? Everytime he dies he turns into ash, the ash the others use to block the MIB. Also he is born again, i.e. as a child perhaps, and he was the kid running through the jungle who MIB and Sawyer saw. He'd come back to make sure that the next Protector was chosen or something like that.
I don't have a lot of hard evidence to back this up but I have wondered about the ash that Ilana and the Others use. Maybe Jacob never really dies and the protector that MIB mentioned is actually someone like Richard Alpert, an outsider who comes to the Island and then takes orders from Jacob on how to keep it safe. Alpert came over on the Black Rock, now the Oceanic Crew came and it's time to pick a new Protector.