I have three websites: two in subdirectories, and one in the root. On the root website, I tried to backup "Both Database & Files" selecting not to backup my own user directory (I keep my personal files outside of the wordpress folders), but only the WordPress directories.
The plugin first of all failed to back up the wp-includes directory. I tried again: same result. I then switched it to "Database only" and it generated a blank file. I switched it back to "Both Database & Files" and now it only makes a backup of the Database. No files are backed up at all. I uninstalled, reinstalled and tried it again, and it does the same thing.
I tried a few other backup programs (like X Cloner) and they work fine on that root website. So there is a problem with this plugin.
The free version, WP Database Backup, which only did the Database, seemed to work fine, which is why I upgraded to the WP All Backup. Apparently that was a mistake.