When Secure Copy job is completed, users observe that a folder has been created at the root of the target volume, even though the option to 'Create initial Source folder on Target volume' has not been enabled:

In the above job, the Target volume would contain the path 'W:\Departments\Departments_Legacy\Departments\, which would then contain the contents of 'Departments' from the Source volume.
Secure Copy 7 introduces a new feature that allows files to be written to the root of a target volume.
• ENH: (US346) When migrating file shares, initial root share folders now created/shared on target
Note: This was not allowed in previous releases of the application.
Workaround 1
Upgrade to the latest version of Secure Copy.
Workaround 2
Un-share the root folder of the source path for the duration of the copy job, so that it is not automatically created on the target. Then enable the shares again when the migration is completed.