We completed a change last year to disseminate users across multiple new Exchange 2010 Mailbox databases (fewer users per individual database).
When completing this we created a new journaling mailbox and data loader per Exchange database.
Since this was completed mail is no longer being shown, within the web console, in the relevant folder as per the users Outlook structure (as an example the Inbox shows the newest mail as what was received before the user mailbox was moved).
The mail is still showing under the relevant user as all mail can be seen when selecting the top level folder.
I figure this is something I have broken while migrating the users but am not knowledgeable enough on the product to figure out why.