Try this
I did a clean install of Leopard and had the same problem with a draft that I would delete and it just kept reappearing and I also had an IMAP account which wouldn't let me delete drafts (I know you have POP).
To solve my problem of the reappearing message, I first tried clicking the drafts folder I was having problems with on the left and going to the menu bar at the top, clicking mailbox, and selecting rebuild. This fixed one problem in my IMAP folders and might work for POP too.
To fix the other draft problem, I couldn't get it fixed using other advice from forums and didn't want to use the terminal, but since I had only one draft I just sent it to myself and that fixed the problem. Sounds dumb but it worked.
Hope this helps someone.