The issue is the MigrateViews setting, which by default is set to 1. There are quite a few internal views in a mail file that reference mail messages (including orphaned documents). When MigrateViews is set to 1, orphaned documents that are locatable by a view are migrated to a folder with the name of the view instead of the "All Documents" folder.
There are two ways to handle this. The simple way is to set MigrateViews to 0. This will disable migrating views, and orphaned documents will end up in the All Documents folder as expected.
The other way is to specifically filter out the views that you don't want migrated. There is a blog article that was written by a member of the migration community that discusses this. He suggests a list of folders that should be filtered. NOTE that Support have not tried these filter settings.
http://seanofarrelll.blogspot.ca/2014/11/folder-filtering-and-mapping-with-dell.html
or
http://seanofarrelll.blogspot.ca/2016/03/folder-filtering-and-mapping-with-dell.html
Please note: That your internal folder names might be different from those listed in the above example.
The preferred suggestion would be to use the MigrateViews=0 method to migrate Orphaned Documents.
