Usually those hard drives work fine with our controllers but you may get in to a compatibility problem and have random crashes of the RAID like yours.
Please go in to BIOS and under the SATA configuration set a hard drive delay, this will allow the hard drives a larger amount of time to initialize and spin up.
If the problem keep occurring then I would suggest to test with different hard drives and test the motherboard out of the chassis to confirm that this is not related to a short or grounding.
I already tested the board with only the cpu/memory/vga/psu and the SSD/HD's with different power supplies (Antec 650 Earthpower Platinum and a Tagan 1000 watts which is the spare for my X7DAE system).
Even then the problem still occurs, i will try the harddrive delay tonight, however i thought that was only for booting the system. If i use the drives without raid1 there's no problem whatsoever with the drives, but when a raid1 config is cerated it's always the second drive that keeps failing.
When the raid is degraded and i click 'reset drive to normal' it gives me an error and i have to restart to make that option work. When it does work it goes into 'rebuild mode' and eventually tells me the drive has failed again.
The 2 WD 2TB drives are connected on Sata Port 2 and 3 (Black ports). The Patriot Pyro SE 240GB x 2 @ raid1 on Sata Port 0 and 1 (blue ports) work perfectly.
I use the exact same drives in my Supermicro X7DAE (Socket 771/DDR2FBdimm - Dual Xeon X5450) setup which also has an older raid controller and they work perfectly there. I believe this is a X5000 chipset that also has the Intel raid (raid bios looks exactly the same).
I also had contact with Intel Tech support, he told me i probably should send the board back for checking, but i'd like to make sure it's not a user error.
Secondly i've tried installing Windows 7 X64 Ultimate when i created a raid1 config in the raid bios and tried it afterwards when in windows using the RTSE tool. This didn't make any difference.
Since i had problems with WD drives and a Highpoint controller before i was thinking this could be an incompatibility issue between the drives and the 'raid controller', however i couldn't find anything similar on the web nor Intel communities.
Service Ticket (8000614093) for reference
Once i tried the Hard drive delay i will post my findins.