Mail will not delete any messages

I have a 10.5.6 server running my mail services. I have a 10.5.6 client checking it. I currently have over 4,000 messages in my inbox and they all get downloaded when I check my mail. If I go to the account preferences in Mail.app and tell it to delete all the messages, they are not deleted. If I go to Get Account Info in Mail.app, I can see all the messages on the server. If I try to delete any of them, they're never deleted.
Now, to get more technical. I telnet into 110 on my server and user the user/pass commands to log into the POP server. Doing a "list" shows how many messages I have and how large they are.
Let's say the last one is 4133 (which it is). I do "dele 4133" to remove the message, then another "list". It shows the message is deleted. I quit out of the pop server, log back in and the same message is there.
Seeing all this, I know the messages aren't getting deleted.
Any ideas why? I have to disable my email until I get this resolved. I currently have 170,000 messages in my client's junk folder (fun times deleting those).

Yes, it was definitely within Cyrus. The Apple interfaces are pretty and all but they didn't even get close to helping me solve this easily.
Essentially, what I did was download all the emails from the server (to make sure I didn't miss anything), rename my email folder to something different to preserve the emails in case I really did miss something, then do a recover on the mailbox.
Being a UNIX-head, here's what I did on the server:
cd /var/spool/imap/user
mv scott scott.dead
sudo /usr/bin/cyrus/bin/reconstruct -r user/scott
Sudo, of course, prompted me for the superuser password but everything was fixed right away after that. It is recommended to shut down the mail service from inside the Server Admin program first.

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Best answer - Sarah (Google Employee) Go to this answer
chessop
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Best regards,
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Please attach screenshots if possible.
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Message was edited by: fireQuartz

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Thank you!
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Mail will not delete any messages

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