Mail constantly checks for new mail; downloads same emails repeatedly HELP!

For the last three days (since 19th), Mail has been downloading the same emails over and over again. I first noticed a problem when about 20 spam emails that usually route to my Junk folder appeared in my Inbox. I thought I had just moved it incorrectly and deleted them, then they appeared again later.
The mail jogger cycle (next to Inbox) keeps turning and turning like it can't stop checking for new mail. How do I get it to stop?? The emails are multiplying like gremlins in my Inbox and driving me nuts!
Also, it only downloads new emails when I first open the app. I have to force-quit out of Mail, then reopen, and I will get a couple of new emails, and then ALL THE EMAILS FOR THE LAST THREE DAYS AGAIN.
Mail was working fine for me until three days ago. The only thing I've changed recently is a Software Update on the 15th for QuickTime and iTunes.
Please help! I tried to Repair Permissions and it didn't do anything. I also tried removing all messages from the server and that did nothing either.
Mail Version 2.1
THANK YOU ANYONE WHO CAN HELP ME!!
iMac G5 Mac OS X (10.4.7) 2.1 GHz, 512 MB Memory

UPDATE: I think I got it to stop checking mail. I have Yahoo mail and I checked my email through online Yahoo. I was able to delete a bunch of emails and it suddenly stopped checking for email in the Mail app.
HOWEVER, it will NOT remove some of my junk emails. I was able to delete over 100+ of them. But one specific message (which I now have 8 copies of) will not go away. It is one of those 'Delivery Status Notification' emails. Is this a virus??
I've tried Erasing Deleted Messages and Erasing Junk Mail. Neither helps. These emails won't go away.
Help please! I would be very grateful.

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Hi, well, POP3 is not designed for keeping the mails in the inbox on the server permanently. Because while checking for new mails, to my knowledge it needs to go through all mails on the server's inbox to check whether it's already downloaded or not.
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this is a very perplexing problem and i have searched forums for how to fix it but as i don't quite know what to call the problem, i haven't found any solutions yet!
i just got a new iMac and proceeded to set up my two gmail accounts with mac mail. one works perfectly fine, the other, for some reason unbeknown to me seeing as both were set up in the exact same way, the second gmail account is stuck continuously checking for new mail with the loading circle next to it.
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FWIW:
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http://www.google.com/support/forum/p/gmail/thread?tid=15f2852996dedf1f&hl=en
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http://forums.macrumors.com/showthread.php?t=776735
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+Possible Solution Found+
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E-mail sending from PL/SQL fails with SMTP error 550 must check for new....

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Mail not checking for new mail

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Mail constantly checks for new mail; downloads same emails repeatedly HELP!

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