Brand new install of Intel Server system P4308CP4MHGC system with C600 RKSATA8 RAID Key and 8 X WD2000FYYZ 2TB Hard drives in a RAID 5 configuration using on board RSTe software RAID with 1 1.5TB partition and the balance (Something over about 10TB).
Install Server 2012 R2 Load RAID Drivers downloaded from Intel website during install in order to be able to see the hard drive partitions. Proceed with the install of Windows without any errors or issues. Install the updated chipset drivers downloaded from Intel site. Device Manager shows no problems.
Continue with windows updates (About 117 in first session, Reboot server, another 116 updates, Reboot server plus another 20 or so updates with 2 - 3 additional reboots. Windows updates Says no more available updates. Also installed the Intel Windows RSTe program to monitor the initialization of the hard drives (This was actually done during the first round of updates). The 1st partition (OS) finishes initializing. Check periodically on initialization of other drive. At last check it got to 35% the second time and about 40% or so the first time. This took probably about 4 - 6 hours (I think this is probably normal for 10TB plus partition?). I don't know at what point it crashed but came back to the computer to find it waiting at the "Troubleshoot" windows screen.
From then on the computer will not see the OS RAID drive but I believe it does see the "Reserved" partition because it begins to start windows and attempts a repair which fails.
Things I have tried: (Including with Microsoft on the phone walking me through some things. They have now said they need to perform additional research and I am waiting for them to call me back). This is the second round with Microsoft support. They tried to help fix the issue for several hours the first time before deciding I should just reformat and re-install which ended up in the same place in the end.
Boot up with the Windows DVD. Can't attempt a repair directly because OS drive not visible due to RAID drivers not loaded. Start Installation of Windows to he point of installing the RAID drivers so that it can now see the RAID array. Then cancel the Installation and go back to the "Install" or "Repair" screen from the DVD. At this point I can now see and work with the OS drive. If I run checkdisk /f it goes through all the options without any errors but BSOD's at the end and instantly reboots. If I run chkdsk without the "/f" option it completes and says there are no problems found.
Microsoft has had me try various things in the Registry such as finding the iastorS.sys entry and changing the parameter to (4) and a few other things all within the System Registry.
I have now installed Windows 2012 R2 twice and gotten to the exact same point after no problems installing all updates and rebooting multiple times etc...
Also possibly of note. I have not gotten to the point of Setting a "Role" for the server or any other configurations. I was waiting for the drives to finish initializing and also the server is not in it's final environment for network configurations etc...