Mail 2.1 re-downloads already downloaded POP mail!

I recently installed Mac OS 10.4.9 on a new Mac Pro tower and my older 15" G4 Powerbook. The OS comes with Apple Mail 2.1. The problem I'm having is with Mail 2.1 regarding retrieving POP mail from the Yahoo server that has already been downloaded. Since I don't routinely clear messages from the Yahoo server, repeating a download from scratch can mean over 9000 messages. This results in duplicate messages piling up in my INBOX.
Since I download POP mail to both of my computers, I don't want to clear the Yahoo server of mail.
How do I prevent Mail 2.1 from downloading already downloaded POP mail without clearing the server?
Powerbook G4 Mac OS X (10.4.9)

The first time to download the messages was 2 weeks ago when I reformatted my G4 Powerbook with the new Mac OS 10.4.9. I then set up the Apple Mail 2.1 to retrieve messages from the Yahoo server. It downloaded all the messages just fine.
Then about 1 week later, when routinely checking for new mail, it started downloaded from the Yahoo server just as it had the first time (thereby creating dulicate copies of every mail message).
This has forced me to clear the Yahoo server, which I really didn't want to do.
This problem is not severe, I understand. But the older version of Mail never had this problem over 2+ years of use.

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Both inbox and outbox from Gmail ends up in my gmail/pop/mail inbox; how to resolve?
- So: the mail I send via gmail comes also in my inbox of mail in which I use the gmail pop account.
Please help!

This is a Gmail issue. Gmail POP access doesn’t work like a normal POP mail server would. Here are some of its idiosyncrasies:
1. Messages downloaded by any conventional POP mail client are marked as downloaded at the server (but not as read on the web), and no longer available to either the same or any other POP mail client.
2. To make already downloaded messages available for POP access again, you must go to Gmail’s Settings > Forwarding and POP page, select Enable POP for all mail, and click Save Changes, which causes everything (and I mean everything) still on the server to be downloaded again.
3. The Mail > Preferences > Accounts > Advanced > Remove copy from server settings have absolutely no effect on the messages stored on Gmail’s server. Gmail ignores any requests to delete messages from the server made by a POP client. What happens to the messages on the server after a POP client has downloaded them is determined by Gmail’s Settings > Forwarding and POP > When messages are accessed with POP setting alone. In the case of Gmail (and only in that case), I recommend turning OFF Remove copy from server in Mail, so that Mail doesn’t even try to remove any messages from the server, regardless of whether you do actually want already downloaded messages to be removed from the server after some time or not.
4. Messages sent using the web interface will be downloaded by your POP mail client as if they were received messages. Although this may seem weird, it's good because it allows archiving all messages locally in Mail, regardless of how they were sent — as long as you don't access the same Gmail account with more than one POP mail client, that is. You can set up a rule in Mail to automatically route those messages to the appropriate Sent mailbox (or to any other mailbox for that matter) if that's what you want.
5. Messages sent using a POP/SMTP mail client such as Mail are also treated as if they were incoming messages for POP purposes, just as in #4. What prevents them from being downloaded is that Gmail marks them as already downloaded immediately. Since they’re on the server nonetheless, already sent messages would be downloaded together with all the other messages on the server if proceeding as described in #2.
6. A particular case of #5 are messages sent to yourself. Instead of putting a copy of the sent message in the server’s Inbox and making it available for download, both the sent and the “received” message on the server are actually one and the same, and hence, cannot be downloaded via POP for the reason explained in #5.
7. Gmail allows POP accounts to be set up in a special way that avoids some of these issues while introducing others. If you only need POP access to the last 30 days of mail, you can configure Mail in “recent mode”, as described in How should I use POP on mobile or multiple devices?, i.e. by typing “recent:” (including the colon but not the quotes) at the beginning of the User Name field (not in the Email Address field) in Mail > Preferences > Accounts > Account Information. Configuring the account this way would allow Mail to download messages marked by Gmail as already downloaded (and download messages sent to yourself in particular), but it would also cause all sent messages (not just messages sent to yourself or through webmail) to be downloaded as if they were received messages.

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I can only send via my ISP provided POP account when at home. I think many ISPs only allow you to send email from their own provided connection. Or is it different symptoms that you see?
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Hi,
Mail is duplicating messages, I have a pop mail account and the preference setting is to erase messages on the server.
Some duplicates are from Nov 2006; after I erased all messages using the terminal and ssh connection.
I was told to rebuild mail index and did it, no improvement.
.......... any help appreciated, I have invested many hours into erasing duplicates ... thanks, Garrett
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1. Quit Mail if it's running.
2. Go to ~/Library/Mail and delete the Envelope Index file.
3. Restart Mail and wait for it to import your existing messages. When that's done, any duplicates or ghost messages should be gone..

Sorry, both at once is confusing in retrospect.
Just meant backup the whole works and drag the current cache & envelope out of their locations to the desktop.
What about the plist?
You can make a Copy of that to move to the Desktop. Sometimes that needs to be made anew also, but requires putting in account info and such, so we generally wait on that one.
What about the files on the desk top?
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I can download and send mail with Thunderbird.
I can't even set-up an account with Mail because it cannot find the POP Mail server.
I have Firewall on with ports 25, 110 and 587 open.
This really seems strange that I can use Thunderbird to set up and use POP Mail access to Cox, but not Mail.
My servers are:
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smtp.central.cox.net
I've followed the steps on Cox's support web site, no success.
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Mail cannot find the POP server
You are using the Welcome to Mail assistant to do this, and when you type in your incoming mail server info it spins the gear a bit, gives an error, and says that if you continue Mail may not work -- yes? What does the error say specifically?
No disrespect at all, but the most likely problem is a typo somewhere / mis-specified username. Please go 'round once more.
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Lately, I've been having trouble with Mail. It just stops downloading mail (but will send) from my server. When I login via webmail, I can always get my mail. I fix this problem by deleting the account from mail, and setting it back up again. Then it downloads all the mail from my server. It seems like after a day or so, it stops working. The problem can't be on my servers end, because it works perfectly. The problem is only in my mail program. I'm getting tired of deleting and re-adding almost every day. Any advice?

If this is a POP account, instead of deleting the mail account, you might get the same results by just deleting the file that Mail uses to keep track of which messages have already been downloaded:
1. Quit Mail.
2. In the Finder, go to ~/Library/Mail/POP-username@mailserver/.
3. Locate one or two files named MessageUidsAlreadyDownloaded and move them to the Trash. Mail 1.x used MessageUidsAlreadyDownloaded to keep track of which messages had already been downloaded. Mail 2.x uses MessageUidsAlreadyDownloaded2 for the same purpose.
Note: For those not familiarized with the ~/ notation, it refers to the user’s home folder, i.e. ~/Library is the Library folder within the user’s home folder.
It’s strange, however, that re-creating the account (or the MessageUidsAlreadyDownloaded file) completely fixes the problem for a while, but it starts happening again shortly afterwards. Does Mail really download all the messages on the server every time you re-create the account?
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"Does it download on some pre-set schedule that can't be changed?"
You can change the times for the +"Check for new mail"+ setting manually or use the computer setting.
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