To check if discrepancy is caused by hidden items run the query below against the Archive Manager database.
Change "YourMailboxID" to the mailbox ID for the user showing the discrepancy.
In order to get the Mailbox ID for the user in AM, you would assign yourself the mailbox, then click on the mailbox. In AM, the URL address bar, there will be 'MailboxID='.
SET @Mailbox = YourMailboxID
AND Hidden = 1)x) t2
GROUP BY MailboxID
Result of first query UniqueHiddenMessages shows the hidden items which are not being collected
Result of second query TotalCountOfMessages shows total count of items for AM archive.
When you subtract TotalCountOfMessages - UniqueHiddenMessages you should get the count of items that Migration Manager for Email Archives collects.