To boot from a volume greater than 2TB, you may need to enable "EFI Optimized Boot" in BIOS.
Here is the hardware
Intel S2600CP4 system board
Intel P4000 chassis
Intel Xeon E5-2620 CPU (dual)
Intel Raid c600 rksata8r5
64gb Kingston DDR3 ECC 1600 memory
3 X 2tb Western digital enterprise (RAID 5)
Bios is updated to the latest version
Set up raid 5 in intel ESRT2 RAID by pressing ctrl+e
Initialized the raid and set the drive to boot
Made a flash drive to boot in EFI for setup of server 2012 standard.
Set the bios to boot into EFI
Start install from usb enter the code for windows
I install esrt2 driver from flash drive
I use shift+f10 to enter the prompt
Dispart, select disk, clean, convert gpt, set partition primary, format fs=ntfs.
Attempt to install windows and get an error that it can not install to this drive because I need to "enable disk controller in bios"
I have set up the bios to use the Raid controller
ACHI Capable SATA Controller: [RAID Mode]
AHCI HDD Staggered Spin-Up: [Disabled]
AHCI Capable RAID Options: [INTEL (R) ESRT2 (LSI*)]
SAS/SATA Capable Controller [INTEL (R) ESRT2 (LSI*)]
It is as if when I boot into EFI windows no longer sees the drives properly.
Unfortunately ESRT2 doesn't support UEFI boot. You'll need to create a VD less than 2TB for OS installation, and you can create a second VD using the remaining capacity for data storage.