Mail 3.5 will not grab all email messages from servers

I may be missing a setting somewhere, but I'm pretty sure I've looked at most everything. When I launch Mail, I currently have a Hotmail Mailbox and a Gmail Mailbox. Neither are functioning 100%. Both have only downloaded a portion of the messages available on the server. The Hotmail account (POP) has downloaded only 140 message, but when it "checks for new mail" it shows it is downloading message 466 out of 466, with 0KB left to go. Gmail has downloaded only 107. I don't know what the total number of email messages is in my gmail account, but it far exceeds 107. What is very annoying is that the Hotmail account is only downloading the oldest messages, as opposed to the newest like Gmail did. I have moved the MessageUidsAlreadyDownloaded3 from the Mail library folder and restarted Mail, but to no effect. Any ideas?

After much searching around and trying different approaches, I finally solved my issue. I ran the combo 10.5.6 updater, and this solved the issue. Prior to running the combo updater, when I repaired permissions several things could not be repaired. After the combo updater, everything works fine, and permissions are fine as well.
My mail issue happened after I updated Quicktime, fyi.

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