Migration Manager fails to upload a fileshare folder, only contents of the folder
Migration Manager should operate the same as SPMT.
If you use SPMT to upload a fileshare (eg \server\shares\administration) to a "library A", the result will be a folder called administration in the library.
If you use exactly the same definition in Migration Manager only the contents of administration will be migrated, not the folder itself.
This shortcoming, makes it very difficult to re-arrange the generally archaic fileshare structure into a more intuitive structure in SharePoint.
Microsoft answer is "well use SPMT". This is not a suitable answer because Migration Manager provides a more central view of your migration project, and the easy ability to share the migration task amongst many agents.