In Sources, select the "client" machine and click on the Options tab. Under Volumes on the dialog there's a dropdown labeled "Back Up:". Set that to Selected Sources, and check-mark the Macintosh HD you think you want to back up. Alternatively, set the dropdown to Startup Volume. Look in the Console at a Backup script while it's running to see if you're backing up the correct Macintosh HD.
I encountered the same problem when I started to backup my MacBook Pro running macOS 10.12.6 Sierra using Retrospect Mac 14.6.0. Adding the MBP as a "client" defaulted to All Volumes in the dropdown, and one of the two volumes is a garbage-named volume which the Engine can't find. I submitted a Support Case about this, but Retrospect Tech Support replied that the garbage-named volume is Apple's fault.