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Right, so it's not that Он не в Москве is gramatically incorrect, it's that it's logically incorrect. It sounds wrong or unnatural not because of the actual sentence structure, but because it simply...

Hah, I wasn't doubting your native speaker's instinct!

Fair enough if you can't explain it, my wife couldn't either, which is why I asked :)

Care to expand on that?

I understand the nom/ gen relationship with negation, but in this case it's not Он, the grammatical and semantic subject, that's being negated, it's в Москве. So why is the...