I assume that you would not consider this to be a problem if Omega was replaced with a 99% reliable predictor. Confirm?
...Huh? My version of Omega doesn't bother predicting the agent, so you gain nothing by crippling its prediction abilities :-)
ETA: maybe it makes sense to let Omega have a "trembling hand", so it doesn't always do what it resolved to do. In this case I don't know if the problem stays or goes away. Properly interpreting "counterfactual evidence" seems to be tricky.
This problem is roughly isomorphic to the branch of Transparent Newcomb (version 1, version 2) where box B is empty, but it's simpler.
Here's a diagram: