Just something that came to me whilst re-watching the finale, i'll try and explain, lets see how i do!
In the first scene, when they are looking out at the Black Rock, Samuel tells Jacob that "it always ends the same" and jacob says that "it only ends once and anything before that is just progress"
Later before Ben Stabs him, Jacob tells Ben that whatever he has been told, he still has a choice.
This leads me to believe that Jacob (like Faraday) thinks that the universe doesn't have to be set in stone. Variables or choice can still change the past and thus the future.
I think he knew about evertything that had happened up to that point, maybe why he never asked to see Ben, as he knew he would be the one to kill him. Is that the time-loop? It starts with the black rock and ends with Ben stabbing Jacob, Both Jacob and Samuel know it's going to happen (like groundhog day) but everytime it starts again Jacob tries to change it, This time he has enlisted the help of Our losties and for all we know, setting off the bomb may change the future? We will only know when season 6 starts i suppose but this is my theory.