Well what you choose may not direct affect what is inside Box B, but there is still a huge difference between the two choices.
Imagine the way that the machine did it's prediction was copying your brain and making this copied brain choose in a simulation. Assuming the copied brain is completely identical to your brain, the machine could predict with 100% accuracy what the real you would choose. In this sense, what you choose can affect what's inside Box B (or rather, what your copied brain chooses can affect whats inside Box B).
One more thing to think about: How do you know that you aren't the simulated brain that's been copied?