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What the issue turns out to be as I learned after opening a pay per incident with Microsoft is that many of my users are above the 5k folder recommendation on Exchange 2003. So each morning all the mobile devices start trying to sync thousands of folders. This causes the Exchange System Attendant to choke up and just stop servicing requests.
I suspect this may have something to do with my Sunbelt Exchange Archiver not performing correctly, since it just started happening after my Domain Controller crashed. and not notifying me, but I'm still not sure of that.
In short, the problem is NOT solved. The only solutions are to upgrade my Exchange server to 2007 which allows 20,000 folders, or to Exchange 2010 which allows 100,000 folders, or go to each user and help them port some of their data into a PST. I'm not interested in moving backwards to PSTs so I will be upgrading my server.