My suggestion is that you turn off the "Store draft messages on the server" in the Account info settings, under *Mail Behaviors.* (Go to Mail Preferences ==> Accounts; or click on the Associated Mailbox and then Right Click to get Account Info. Either approach will get you to the property pages where you will see the Behaviors tab)
I noticed this with Gmail (using IMAP) and it appears that by default, Apple Mail will save a draft EVERY 30 seconds. I had a Blackberry that was also set up as an IMAP device and although I only SENT one message, it was causing multiple messages to be sent to my Blackberry. I would have a new message every 30 seconds while I was typing my new message or even on a reply.
There were also multiple messages in the Trash from the same message as it was being composed.
Whether this was caused by settings on the Blackberry, I never really pursued, but unchecking the "Store draft messages on the server" solved my problem.