Messages being scanned by the Exchange Store Manager Service are going to a folder called JournalReportsxxx and not the Inbox folder.
The Exchange Store Manager Service is not on or not properly scanning the mailbox (es).
Upgrade to version 5.1.2.
Confirm the Exchange Store Manager Service is running
Look at the ESM worker log and determine if the mailbox in question is being scanned.
To find the MailboxID.wlog:
a:) From Administration Console | Go to Mailboxes in Left Pane
b:) Search for the user mailbox in right pane and choose edit blank out the "last folder updated".
c:) Go to Archive Manager Services console and stop and start Exchange Store Manager Service.
d:) Give yourself rights to the mailbox by searching your name at bottom right hand corner "Find User" Column and "checking" your account.
e:) Go back to Archive Manager in top right hand corner
f:) You should now see that mailbox under your own Website.
g:) Click on the root of his mailbox.
h:) Address Bar of your Explorer will tell you the Mailbox id.
Now that Mailbox is available to administrator.
Go to AM server and browse to ESM folder on AM server, go to today's date folder search for that Mailbox id and check the Wlog.