How many users do you have total that are working on the new Exchange 2003 box?
Are you running Exchange 2003 SP2? If so, BES 4.0.0 does not support SP2, only BES 4.0.4 and higher supports that version of Exchange.
How were the mailboxes moved? Do you see any errors for those users in the MAGT log?
What happens when you run IEMSTest for those users?
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