Just a thought, but what if jacob is locking Ben out, as a punishment. Ben may have communicated with him at one time, and then had a falling out. We really don't know waht preempted the strike on Dharma, I mean, why right at that moment did Ben decide to start the 'mission'. It may have nothing to do with it, but who knows.
Ben may have encircled the shack with Ash to keep Jacobs smoke monster from killing Ben while he visited, or tortured, Jacob.. Or maybe the dust was magnetite(sp?), and acts like the fence around the Barracks... That may be why Ben was nervous to go to the shack, but seemed fine once he was beyond the mysterious ashen border.