"Wait though. Even if Smith is a one-boxer, now that I've fixed what will be in the boxes, Smith is better off two-boxing. Smith is smart enough to realise that two-boxing is dominant, once I can't causally affect the contents of the boxes." So Omega doesn't put the money in the box.

That line of reasoning is though available to Smith as well, so he can choose to one-boxing because he knows that Omega is a perfect predictor. You're right to say that the interplay between Omega-prediction-of-Smith and Smith-prediction-of-Omega are in a meta-stable state, BUT: Smith has to decide, he is going to make a decision, and so whatever algorithm it implements, if it ever goes down this line of meta-stable reasoning, must have a way to get out and choose something, even if it's just bounded computational power (or the limit step of computation in Hamkins infinite Turing machine). But since Omega is a perfect predictor, it will know that and choose accordingly. I have the feeling that Omega existence is something like an axiom, you can refuse or accept it and both stances are coherent.