We have found three possible causes for this.
1. If your Internet connection is broken during download the messages you've already recieved will be sent again.
2. If your E-Mail program is set to check for mail every 1 minute or a short time period, and you have a large file that could not be downloaded within that time frame, then when the time frame completes and the next time frame begins the e-mail program would break the connection, put the email in the inbox and go to download it again even though the previous download did not complete.
3. If you have an e-mail stuck in your mailbox that will not allow the download to complete. See Below.
All of these are due to the fact that the server will not delete the messages until your e-mail program reaches the end of your download and sends confirmation to the server that it has recieved everything. It is at that point that the server deletes the messages from your mailbox. This is actually a good thing as it prevents you from losing messages that you don't recieve.