Rsync not syncing

Not so much an idiot, as the lack of the trailing slash is the default and the way the backup jobs do this isn't well documented.  You have to actually go in and edit the destination after creation to add the slash.

Here is why it does what it does:  Say you have ThisStuff and ThatStuff directories to backup with different backup jobs.  If you back them both up to Backup and it put everything at top level, it'd get all mixed in.  That would be especially a problem if you have it set up to delete files in the backup that are deleted on the source -- each job would delete the files of the last.  So, it backs them to Backup/ThisStuff and Backup/ThatStuff.  Of course, each job doesn't know if others exist, so it always backs up to a sub-directory named after the source.  A trailing slash can be added to eliminate that, but you have to expressly do it, to assure that's what you really want.

Your first backup was likely by some other means (maybe drag-and-drop), so the files and directories you currently have at top level are very old (but a lot are probably duplicates).  But their presence confused you as to where the newest stuff should be.