The number 1033 is prime. The rest of the hypothetical scenario is pretty confusing, and it'll take me longer to analyze it and be confident about my conclusion than it did to determine that 1033 is prime.
You just got run over by a trolley. Death is almost certainly worse than either being given a free $1M or $2M. This illustrates that failure to consider the decision being made is in general a sub-optimal game-theoretic strategy. Fortunately Omega pays out despite your failure to take any boxes (before your demise) and so your heirs gain an additional $1M. As for your timeless influence on Omega's decision: by the wording given ("IF ... AND IF" instead of "IF ... ELSE") Omega is free to choose whichever number he likes given that neither criteria is satisfied.
Rest in Peace.
You see two boxes and you can either take both boxes, or take only box B. Box A is transparent and contains $1000. Box B contains a visible number, say 1033. The Bank of Omega, which operates by very clear and transparent mechanisms, will pay you $1M if this number is prime, and $0 if it is composite. Omega is known to select prime numbers for Box B whenever Omega predicts that you will take only Box B; and conversely select composite numbers if Omega predicts that you will take both boxes. Omega has previously predicted correctly in 99.9% of cases.
Separately, the Numerical Lottery has randomly selected 1033 and is displaying this number on a screen nearby. The Lottery Bank, likewise operating by a clear known mechanism, will pay you $2 million if it has selected a composite number, and otherwise pay you $0. (This event will take place regardless of whether you take only B or both boxes, and both the Bank of Omega and the Lottery Bank will carry out their payment processes - you don't have to choose one game or the other.)
You previously played the game with Omega and the Numerical Lottery a few thousand times before you ran across this case where Omega's number and the Lottery number were the same, so this event is not suspicious.
Omega also knew the Lottery number before you saw it, and while making its prediction, and Omega likewise predicts correctly in 99.9% of the cases where the Lottery number happens to match Omega's number. (Omega's number is chosen independently of the lottery number, however.)
You have two minutes to make a decision, you don't have a calculator, and if you try to factor the number you will be run over by the trolley from the Ultimate Trolley Problem.
Do you take only box B, or both boxes?