Since the problem is pitch related, it could be some sort of 'wolf' note: it may have developed a resonance at that pitch which 'plays badly' with the rest of the guitar. It could also be any on of a number of things such as you have already checked. I've had terrible buzzes caused by very small loose parts, and these can be a nightmare to track down. The only consolation is that, once found, such things are often easy to fix.
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