Some things to look at:
The qmail &/or qpsmtpd log files should indicate if the server is actually delivering multiple messages to you, or if it is only delivering a single message that is then being mis-handled by something else. If you're getting multiple emails delivered to you I'd look through the notification settings for the various servers -- are they sending to a group or mailing list instead of a single mailbox (or anything like that)?
If you've ever had any of the mail sorting options setup, maybe you have an old rule that is misbehaving.
Likewise for your mail client (if you have a rule to file these things automatically, maybe it's misbehaving).
If you're using fetchmail, perhaps the message is being mis-handled by that process somewhere.