Mail 3.6 downloads multiple copies of emails from my pop account

Since I auto-upgraded to Mail 3.6, Mail is downloading multiple copies of email from my pop mail account. This did not happen before and I haven't changed any of the mail settings. I have read discussions about a similar problem with an earlier version of Mail and the solution seemed to be deleting some file linked to Mail so it could be rebuilt, but I can't find such a file on my system that I could try deleting.
It may matter that I am not 'strictly' supposed to be using os x 10.5.8 on my powerbook G4 (according to what is said on the packet).
Help please!

@ Tokyodj
Thanks very much for posting this. I was having slightly different issues than the people above - only one of my two POP accounts was being constantly picked up, and I had hundreds of versions of each email... strangely, even after I went to the (Yahoo) account and deleted all the emails out of there. Your solution worked perfectly.
Thanks again!

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