Hi, I had this problem, or a variation of it anyway. In my case it was not that I was "receiving" the emails, but somehow they were being copied. I know there were times where I would move a group of emails to a folder (on my mac) by control click > move to > [selected folder] There were times that I would swear that I selected move to but they would not go anywhere, I later discovered that the the messages were being copied by going to Mail <Edit> and seeing that it said "undo copy messages" The other thing that I have not substantiated, but I suspect may have copied messages was when I would change a rule's "move to" destination mailbox, and applied the change.
I hope you find answers for your particular problem but in the mean time, I can recommend some Mail scripts from "Andreas Amann's Freeware", one of which easily found the duplicate messages and moved them to one location. You can find them here:
http://homepage.mac.com/aamann/
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GL,
Kevin