BackupBuddy FTP destinations are inconsistent

I have my destinations set to a certain folder I setup, but…
-the files are not sent there
-they are sent to wp-content/uploads
-and strangely, the sometimes are sent to the root of my host as well. Not all the time but there’s a few duplicate files there.

Whats up?

https://wordpress.org/plugins/better-wp-security/