The only time I have seen mail repeated is when an e-mail client (In my case outlook) times out while downloading several messages at once. It then does not mark the first message (that had downloaded before the timeout) as downloaded and then downloads it again.
A similar issue can occur when a remote site is sending a message to your site via SMTP. If the remote site disconnects before your site says that it has completely received, checked and saved the message, the remote site will later resend it. Meanwhile, your site might have saved the message into your folder. Very slow virus/spam checking and very large messages can make such problems more likely.
Study of mail headers of repeated messages and qmail and qpsmtpd log files will reveal if this is what the problem is. The signature in the mail headers is that the messages will be identical, including Message-Id, except for the locally added Received headers.
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