The simulated you will presumably not gain $1K/$1M worth of utility from taking the simulated $1K/$1M (if it does, then it's a different problem).
Why not give the simulation $1K/$1M simulated dollars? Last I heard simulated dollars are fairly cheap when you're running the simulation. Omega is possibly lying by omission about the fact that the simulation is going to end at some point in the future, but that's hardly news. Nor even strictly necessary.
Just developing my second idea at the end of my last post. It seems to me that in the Newcomb problem and in the counterfactual mugging, the completely trustworthy Omega lies to a greater or lesser extent.
This is immediately obvious in scenarios where Omega simulates you in order to predict your reaction. In the Newcomb problem, the simulated you is told "I have already made my decision...", which is not true at that point, and in the counterfactual mugging, whenever the coin comes up heads, the simulated you is told "the coin came up tails". And the arguments only go through because these lies are accepted by the simulated you as being true.
If Omega doesn't simulate you, but uses other methods to gauge your reactions, he isn't lying to you per se. But he is estimating your reaction in the hypothetical situation where you were fed untrue information that you believed to be true. And that you believed to be true, specifically because the source is Omega, and Omega is trustworthy.
Doesn't really change much to the arguments here, but it's a thought worth bearing in mind.