Several of my friend and I once had a similar problem on some PC's using Outlook Express. We all had Norton Anti-virus installed and set to scan incomming messages for viruses. The problem turned out to be an e-mail with a virus attached to it. When Norton detected certain viruses it would freeze. This would cause your computer to have to start back at the beginning to retrieve your messages.
Since e-mails are only removed from your service provider's server after your computer tell's it that it has successfully received all of the messages, the messages would not be deleted. Basically since the complete list of e-mails were not retrieved, the server would not be told to delete them.
The way we solved the problem was by checking our e-mails with a web based e-mail site. The one we used is:
http://www.mailstart.com/
This site will allow you to check your e-mail account once a week for free, if you want to use it more frequently, they charge a fee. This will help in a couple of ways, first it will allow you to delete the problematic e-mail, second, it will allow you to read your message before you delete it.
All you need to provide them is your e-mail address and password, then it'll retrieve your mail. Works just like a hotmail account.
I don't know if there are other sites out there with similar capabilities, but atleast this might get you started.
Hope this helps.
Michael Hunter
hunters2@mac.com