To clarify ..
Is the mailbox currently over it's send/receive limit?
If that is the case then enterprise vault can't archive anything in that mailbox.. you'd have to temporarily increase the quota slightly. During archiving the first thing we do is effectively take a "copy" of the mail, and then add on some extra attributes like archive date, saveset ID and so on. If the mailbox is over the send/receive limit, then we can perform a "save" operation on those messages (so we roll back the change). Likewise for synchronisation, we delete the current hidden message in the mailbox which is just a couple of Kb in size, and create a new one, but if you're over quota, then we can't create the new one.
Unread Mail is a search folder, and Exchange doesn't guarantee keeping them up to date... the indices for search folders also consume space in the mailbox. Both might be the reason it's not updating.
Hope that helps,
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