Mail is restoring thousands of messages to inbox

I upgraded from Tiger 10.4 to Leopard 10.5.8 about a month ago and have been running Time Machine.
I move my mail from my inbox (I have several accounts) to different topic files, so that I don't have more that about 100 messages in the sum of my inboxes. I never delete messages, so this has nothing to do with the trash.
Searching the contents of mail didn't work, so I tried rebuilding the accounts within the inbox.
Now here is the weird thing. If I look at the Time Machine backup of ~/Library/Mail/POP-<account>, I see that there have been about 6000 .emlx files in the folder, but I only saw about 50 to 100 of these at any one time.
When I did the rebuild, it gradually increased the number of files in the folder to about 11000. It must have been getting these from the folders to which I had moved the messages, because I had taken mail offline, so it couldn't be getting them from the POP mailbox. When the rebuild was finishing, the status line in the window header said about 6 billion messages.
Now that the rebuild has completely finished, it says 143 messages 88 unread, but there are still 6241 .emlx files in the folder.
This is really weird. What on earth is going on?

Well, I moved the 143 messages to another mailbox, so that account's inbox was empty. (These messages were all really old ones, not recent ones) Then I rebuilt that account's inbox. Again, the folder on disk grew to over 11000 messages, then reduced again back to 6241 .emlx files. When the rebuild had finished, there were no messages showing in account's inbox, despite the 6241 files in the folder.
Then I quit Mail, removed the Envelope Index file, and then restarted Mail to re-import all the mail (in accordance with http://docs.info.apple.com/article.html?path=Mail/3.0/en/14019.html). Towards the end of the import, all 6241 files were moved across from the old inbox messages folder to the new one (with all new .emlx file numbers).
So mail really thinks those files should be there, but doesn't show them in the inbox. I really don't understand where Mail is getting the details and locations of the messages for restoring them (even temporarily) to the inbox!!
The only unusual thing is that the POP account on the server has some 14,000 messages. There are actually two MessageUidsAlreadyDownloaded files, the second called MessageUidsAlreadyDownloaded2.

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This is a werid one but hoping somehere here can help or at the very least someone from Apple is listening.
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13" MacBook Air - Mid 2011
13" MacBook Pro - Mid 2012
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MateoV wrote:
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Kurt,
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I have a proper mailing list created as the manual says. It's a small group of contacts that exist in the address book. I do not type them as CC I just write "clients" and before I finish the word the name of the list appears.
How can I stop Avast from scanning out going mail? It's the free version and I haven't found a real solution. I also tried to totally turn off the "mail shield" but I kept facing the same issues. However, I just turned it off and tried to send the mail, I didn't restart windows or thunderbird
The idea with ipage server was fantastic! It would never come to my mind!!! As far as I see, the limit is 250 mails per hour. I doubt if I have ever reached the 50% of it. I also don't reach the bandwith limits... Besides that, if I had exceeded the limit I would get multi responses that "mail was not delivered".
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Message was edited by: Atlantax

FromBone wrote:
Thanks V.K.! So there is no chance for me to re upload all the messages from my mac to my yahoo inbox.
nope.
May I ask yahoo to that?
you can ask but they won't say anything different.
I could never have known that the default setting on mac's mail would be "remove copy from server after retrieving a message".
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http://www.apple.com/feedback/macosx.html
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XMLA

I'm having the same problem and have only noticed it since upgrading to 10.5.7. I've tried rebuilding the mailbox a few times, disabling the GrowlMail bundle, vacuuming Mail's SQLite database, and even tdeleting the account and starting over. (It's a Gmail account I connect to via IMAP.) And yet:
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Mail is restoring thousands of messages to inbox

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