Can you post Screenshots of the "Settings" page & a screenshot of the "Create A Backup" page.
The only thing I can think of is that for some reason the variable did not save properly on your site for the folder that its supposed to archive ("Currently Archiving")
"Currently Archiving" should indeed be your full path to the folder or full site
ex: Currently Archiving: /aaa/bbb/ccc/wp-content for content only
ex: ex: Currently Archiving: /aaa/bbb/ccc for full site
I also just did a clean install of WordPress EZ Backup 7.0.4 on a MU site and the paths were gathered correctly.
On a MU Site the root path will be the same for each site since they are all under one path. Backing up wp-content only will of course backup every site in that MU install due to how WP stores each site. Same effect as backing up the full site etc.
If you would like I can use FTP and see exactly what is going on with your site. That is entirely up to you. If you wish to let me take a look please e-mail me your information