Recently, I attempted to install Windows 2012 Server to a 3Tb Intel RSTe RAID. The motherboard I was using had a C600 chipset and its BIOS supported EFI booting in addition to legacy booting.
Legacy booting implies MBR booting. This subtlety should not be overlooked.
I merrily accessed the server's BIOS and set my boot order. I wanted to be sure to boot from optical first, then the RAID. I figured I could set the optical first in the boot order, then EFI in order to get what I wanted, without any ambiguity relating to the optical drive.
Sure enough, I booted up to the Windows 2012 Server DVD in my optical drive, as intended, and it was off to the races. As I continued, the install process asked where to install, "the RAID!" I answered. The install process then showed me a 2Tb RAID with the balance (I had a 3Tb RAID5) unusable.
"That's weird," I thought, "must be an MBR thing. Alright Windows, do your thing and we will take it up in disk management after the fact."
No such luck, disk management would not let me convert to GPT. So, I'm throwing away storage my client had paid for.
How we lookin'? NOT GOOD.
Remember the statement, "Legacy booting implies MBR booting. This subtlety should not be overlooked."? What happened to me (and maybe you) is once I set the optical drive as the primary boot device (legacy) in the BIOS, my goose was cooked. The answer to my problem was to set EFI as the primary boot device, with the optical drive as the primary within EFI.
Once I made this change, the Windows installation invoked GPT support and I had the full capacity of my RAID5.