IMAP email not appearing in Mail

Background: I have an IMAP email account that's over a decade old.  It's going away soon so I'm trying to figure out how to get a complete local copy of all that email.  There are a total of around 100 folders with anywhere from 5 to over 2000 emails in each folder.
The problem: there's email on the server that isn't showing up in Mail.  For instance one folder (according to the webmail interface) has 771 messages.  Mail says that folder has 700 messages.  Looking at the webmail interface I can easily find several of the 71 emails that are not appearing in Mail.  In Mail, if I select the folder and "Get Account Info" and look at the Quotas section, it lists the correct number of email messages (771).  If I rebuild the folder, as it's being rebuilt the blue progress bar at the bottom left of Mail says there are 771 incoming messages.  But when it's done, I can only see 700.
I just double checked on a second computer (MacBook Pro, also latest 10.7 version & Mail) and it's the same there, it only sees 700 messages.
Now, repeat this times the roughly 100 folders . . .
What's going on here?  Why isn't Mail downloading or displaying these emails?

I just looked in the User/Library/Mail/V2 folder, and tracked down this folder.  Digging down several levels into the files for this account and folder I found two sub-folders called "Messages" which contained a total of 774 (mostly) .emlx files.  In three cases there were a pair of files with the same number, one with an .emlxpart extension and the other with a partial.emlx extension -- if I assume that pair corresponds to the same email, this it appears there are 771 messages on local disk.  And Mail refuses to display 71 of them? 
I'm doing a backup with MailSteward to see what it makes of these files.

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