I have a Windows Server 2012 Essentials setup with 4 x 1TB disks. I needed to reconfigure my backup settings because one of the disks had grown and so did the backup disk up to maximum capacity (In other words, it was full). I decided that I wanted to leave out the whole disk all together but Set Up Server Backup forced the backup of the disk with the following message: Server Backup requires that you back up this item to ensure that you can restore the operating system in the event of a catastrophic failure.
I didn’t understand the reason till I remembered I installed MDT (Microsoft Deployment Toolkit) and WDS (Windows Deployment Services) and the last one caused the problems. Because Backup sees a system service is using the disk, it will include this disk to the Back Up selection. It’s not possible to select just the directory that is in use by the specific service.
After moving the WDS RemoteInstall directory to (In my case) the D: drive, I could deselect the original drive from the Back Up selection.