I wonder if your issue is related to one I recently had .... I would save an email as a draft and when i sent it off, I'd find 2 copies still in the Draft folder. It seems to have sorted itself out but I did google it and there were several instances of the same or similiar issues.
I have never seen your exact issue but had one back in Panther (10.3)'s email where I had 2 inboxes. Forgot what I did but it went away. It's been ages.
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