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I think its every affiliates nightmare to be processing payments and end up short

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Um, don't send out payments until you have everyones results and make sure they add up? If they don't add up, you can have everyone send their hand histories and do the numbers yourself. If they still don't add up, you can spot check hand histories with Party until you've found the cheat.

Is this a PITA? Yes. But you signed people up with the expectation of getting their RB, and you have an obligation to try and deliver on that promise. If you clearly explain that cheats will eventually get caught and forfeit their rakeback, I think you won't have too much trouble with your players trying to game the system.