Turns out Server 2008 R2 installed the System Reserved Partition (100MB) on the RAID array that I setup for DPM 2010 backup storage and not on the mirrored system partition like it should have. I could not convert the array from MBR to GPT that is required for disk arrays over 2TB until I got that partition off of there.
Here is how to delete the partition:
1) Open a command prompt with administrator privileges (right click => run as administrator)
bcdboot c:\windows /s c:
You should get a message similar to:
Boot files successfully created.
2) Open the Disk Management GUI (you could use diskpart for scripts), locate the C:\ partition right-click and select “Mark Partition as Active”, select yes to the “do you want to continue message”
3) Reboot to confirm that everything is ok.
4) In Disk Management you can now delete the 10…