Mailboxes are showing up in collections even though source and target AD user objects and their corresponding mailboxes have been deleted

Quest Migration Manager needs to be able to read the deleted objects container in order to confirm the deletion of an object and stop it showing in a mailbox collection. If the agent service accounts do not have permission to read this container then deleted objects may remain

Please follow this solution in order ot grant the QMM service accounts the ability to read the deleted objects container:

How to let non-administrators view the Active Directory deleted objects container in Windows Server 2003 and in Windows 2000 Server: - http://support.microsoft.com/kb/892806/en-us