Why are all my resources showing in the top block of my restored course?
The problem with all of the resources showing up in the top block seems to be the result of, during the restore process, choosing a setting of: restore to: existing course adding data to it
You should choose: existing course: deleting it first when you do the restore.
If this has happened to you and you have all of your files in the top block, redo the restore the correct way (choose existing course deleting it first). This should overwrite the existing files.