Saved folder sometimes is nested one level down?

I have a strange problem. I backup to a Synolgy NAS on my local network. I have mapped various NAS drives to drive letters on my backup server. Randomly I get the backup copied to a folder one level down. This results in essentially a backup 2x larger than it needs to be. It normally looks like this:

S:\Media
______\file1
______\file2
________.
________.
________.

But when it nests down one level I get this:

S:\Media
______\file1 (old)
______\file2 (old)
______\Media
____________\file1
____________\file2
_____________.
_____________.
_____________.
______\file3 (old)
________.
________.
________.

(I had to put all those underscores in there to preserve the formatting)

All of the files under the nested down Media folder are duplicates of the ones above, except new or changed files which don't get updated at the higher level.

It's kind of a big deal when the Media folder is 300GB and takes >10 hours to back up from scratch.

Why is this happening?

Thanks.