I believe the "magic box" is actually going to be a reference to the mathematical "Golden Rectangle" (the idea of divide a square out of any rectangle and you end up with a rectangle of the same proportions again - infinity...) The Golden Rectangle was seen on the "fake" hatch door at the Pala Ferry site. I think that hatch is going to turn out to be a real hatch, an important-to-travel-to-the-island hatch ~ which might explain why people need to be drugged for that terrible last leg of the trip (if you traveled regular-style to the island, on a boat or sub, you would need to use the restroom, eat, and drink~ which you couldn't do if are knocked out cold). The trip has to be short, so I think something is going on inside that "fake" hatch.)
Flaneuse - you make a very salient point~ Locke was pursuing something, but it (finally) wasn't his father - he was going on the walkabout. James, on the other hand, was in Australia, still carrying a letter he wrote when he was 8 years old, still searching for a man, still calling himself that man's name. Ben thought he had a handle on the situation, and yet, unbeknownst to him, nature "course corrected" on behalf of James. Ben does believe that one proves their commitment through the demonstration of free will (choice), Ben needs people to chose to (fill in the blank - do whatever Ben wants). But Ben's idea of free will is false - it is not a "true" free will in that Ben alters the situation, tampers with the variables, manipulates the situation to guide a person to make the choice Ben wants. So in the Locke/James scenario I believe Ben will get a shock - the result (Cooper dead) might appear to be the what Ben wanted, but the method was not (Locke didn't do it), and Ben is unaware of that.

__________________