Why is whether your decision actually changes the boxes important to you? [....] If you argue yourself into a decision theory that doesn't serve you well, you've only managed to shoot yourself in the foot.

In the absence of my decision affecting the boxes, taking one box and leaving $1000 on the table still looks like shooting myself in the foot. (Of course if I had the ability to precommit to one-box I would -- so, okay, if Omega ever asks me this I will take one box. But if Omega asked me to make a decision after filling the boxes and before I'd made a precommitment... still two boxes.)

I think I'm going to back out of this discussion until I understand decision theory a bit better.