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I have a new installation of exchange 2003 and in the mailboxes of some of the users there folders are empty from the inbox down. I moved the folders from an IMAP account on an old server into the mailboxes. the folders are there but no mail in them. In the bottom right hand corner of the screen there is a folder update thing running but it only does the ones up from the inbox. 
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I have a new installation of exchange 2003 and in the mailboxes of some of the users there folders are empty from the inbox down. I moved the folders from an IMAP account on an old server into the mailboxes. the folders are there but no mail in them. In the bottom right hand corner of the screen there is a folder update thing running but it only does the ones up from the inbox. 

exchange 2003 mailbox folders empty from the inbox down

Interactions between email servers and clients are governed by email protocols. The three most common email protocols are POP, IMAP and MAPI. Most email software operates under one of these (and many products support more than one).  The correct protocol must be selected, and correctly configured, if you want your email account to work.

Email Protocols

Exchange is the server side of a collaborative application product that is part of the Microsoft Server infrastructure. Exchange's major features include email, calendaring, contacts and tasks, support for mobile and web-based access to information, and support for data storage.