I think I have figured out what my problem is. I am running Server 2012 R2 on an HP n54l. I have my OS drive installed in the optical drive bay which connects to the optical drive SATA port on the motherboard. I also had one of my 2TB hard drives installed in the first drive bay when I installed Server 2012 R2. Since the 2TB drive was installed on the first SATA port "Disk 0" in the PC, from what I've read, Windows will always place all operating system boot files on this drive even if you install the OS on a drive on a different SATA Port. So, if I had removed that 2TB drive before installing my OS I wouldn't have had this problem. Fortunatly, it looks like I may be able to fix this issue without reinstalling. I found the following tutorial on www.sevenforums.com which I hope will also work on Server 2012 R2.
http://www.sevenforums.com/tutorials/105541-startup-repair-run-3-separate-times.html
In a nut shell, it looks like I just need to mark my OS drive "C:" as active, then remove all other hard drives on the server. Then boot into my Server 2012 R2 installation disc and choose the "StartUp Repair" option in the System Recovery Options menu. The tutorial says I may need to do the StartUp Repair up to 3 times to get all the necessary boot files to be written over to my OS drive. Once I have Server running correctly off of just my C: drive, then I should be able to reformat my 2TB drive, to get rid of the unneccessary boot files stored on it, and add it back to my mirrored StableBit Pool. Once this is all complete, I am hoping that Windows Server Backup will no longer require me to include this 2TB hard drive in my Bare Metal Restore backup!
I really hope this works...LoL