If the following sequence of events occurs for a user, Sharepoint Processing Wizard will not update their permissions:
1. The user is added to the Sharepoint permissions database
2. The user is then renamed (including their samaccountname)
3. The user is then migrated with QMM
This problem occurs because Sharepoint caches the samaccountname that was present on the object when they were added to the Sharepoint database. The Sharepoint Processing Wizard updates permissions based on the user's current samaccountname.
Therefore, no match is found (because the samaccountname has changed) and the permissions are not updated.
At this time there is no workaround for this issue. The Sharepoint processing wizard uses the API provided by Microsoft which only supports usage of the samaccountname attribute to update the database. At this time Microsoft only supports usage of their own APIs against Sharepoint databases.
A change request, CR57813 has been created for this issue.