I have a problem with my ICH9R. Setting up the array and installing Windows works fine, but whenever the system restarts the raid-bios hangs after detecting the first 3 drives allthough it reports 4 drives is connected. The cursor blinks and the the system will restart with ctrl-alt-del. I have 4 x WD-5000AAKS in raid-5. (Raid-0 gives the same result.)
 
Since the raid-bios hangs I can not enter BIOS or either of the other configs (2 x sata onboard controller (ctrl-i, ctrl-g)or network)
 
The only way to get the system going again is to disconnect the failed drive. Connecting the drive to any other port on the ICH9R will not help.
 
To fix the array I need to connect the disk to another controller and format the disk (or erase it completly with Western Digital Dignostics tool). Now connecting the formated drive to the array I can add it back to the raid-5 array. It will rebuild just fine, but restarting will hang the bios and the cycle continues. Argh!
 
Testing the drive with Western Digital Dignostics Tool (full scan and SMART) gives the thumbs up.
 
Any idea on how to resolve this?

After setting up the raid configuration on the next restart enter the BIOS and in Boot Configuration select the raid array as your primary hard drive to boot to Windows.

Good advice zpyrd, men thats not the case as the drive isn't properly detected and hangs the BIOS. I am not able to enter det BIOS with the failed drive still connected.  
 
Formating the drive on another controller fixes this as I wrote earlyer.

I'm not sure what could be causing the problem.
I'm familiar with RAID configurations and I haven't experienced troubles like you are having. However the largest RAID configuration I have done on a 32bit desktop PC is 500GB.
 
It's possible there is nothing wrong the fourth drive. Maybe the RAID controller of the ICH9R is limited in it's capacity to address 2TB of storage. But I think that is unlikely.
 
From what you have posted I have gathered you can boot into Windows with three drives attached?
When you add the fourth drive all is ok?
While in Windows you can rebuild your array with four drives attached?
When rebooting after rebuilding the four drive configuration the BIOS hangs while identifying the fourth drive connected?
 
Are you using the Intel Matrix Storage Manager to configure your drives?
 
If you are, are you using the latest version available from Intel?
 
Also are you using the latest BIOS update for your motherboard?
 
Have you used the BIOS CMOS jumper on your motherboard to enter the BIOS in configuration mode? With the BIOS jumper connected to the BIOS configuration pins when you start your computer the computer should automatically boot into the BIOS configuration tool. With the BIOS configuration tool open you should be able to identify all your hard drives connected, identify the RAID configuration and set the RAID array as the primary drive to boot to Windows.
When you save the BIOS changes you will be prompted to place the BIOS configuration jumper to the Normal position and to do a manual restart. And hopefully the BIOS will not hang on the fourth drive and boot into Windows normally.
 
What model motherboard do you have?
 
Is your optical drive SATA? If it is do you have it connected to SATA port 5?
 
ICH9R natively supports six SATA ports. I assume you have your hard drives connected to SATA ports 0 thru 3. It should not matter if one of the SATA ports is identified as e-sata. The BIOS identifies SATA the same. The BIOS doesn't identify a SATA port as internal or external nor does the BIOS give an e-sata port any special identification or controls except you may be able to deactivate the e-sata port for security.  
 
I hope all works out. If the problem still occurrs I hope someone else will post more helpful tips.  
 
My next suggestion is probably something you don't want to do.
And I don't recommend doing this until all options, resources and helpful tips have been exhausted to no avail of solving your problem.
 
Disconnect all the drives.
Connect a hard drive to SATA port 0.
Format the drive and install Windows, all system drivers and Windows updates.
Connect the other three hard drives to SATA ports 1, 2 and 3.
In Windows disk management format the hard drives connected to SATA ports 1, 2 and 3.
Use the Intel Matrix Storage Manager to set up your RAID configuration.
When the storage manager completes your RAID configuration you will be requested to reboot the computer.
On reboot (hopefully the BIOS sees all four hard drives) enter the BIOS configuration utility. In drive management or boot configuration choose the RAID array as the primary drive to boot into Windows.  
Save Changes
Hopefully your computer will boot up normally and Windows will start and you will have your four 500GB WD hard drives in the RAID configuration you want.
 

First: Thank you for such a comprehensive reply!
 
Second: All in quote is correct.

 
Yes, I'm using Intel Matrix Storage, latest edition, but no, I have not upgraded BIOS yet.
 
Motherboard is P35-DS3P with Q6600. There are 6 sata ports on the ICH9R controller. I use port 0-3. I've tried other combinations as well. Nothing else is connected to the ICH9R.
 
Since this is a new computer with nothing importent data stored on it, I will take everything apart for the N'th time.  
 
If it's not a seccess I will update the bios.

The problem has been resolved. (Thanks to zpyrd for his advice.)
 
One or more of the following has done the trick:  
 
Updated BIOS to v6.00
Removed Intel NIC (Intel Pro 1000GT)
Installed newer Intel Matrix Storage Manager: 7.8.0.10.13 (previous was 7.8.0.10.11 I think)
 
I guess the BIOS did the business. So everyone who is planning a Raid-5 array on ICH9R with more than 3 drives - update your BIOS.

I just moved a RAID-1 array from JMicron (JMB63X) to Intel (ICH9R), and want to make sure I've got the latest BIOS/drivers.
 

 
Do you mean your motherboard BIOS?  (Is there a way to upgrade the ICH9R BIOS apart from flashing a new mobo BIOS?)
 

 
Just wanted to confirm: did you mean 7.8.0.1012?  That's the latest MSM version I could find, at least on Intel's official site:
 
http://downloadcenter.intel.com/fi [...] bmit=Go%21
 
Thanks to all for the helpful input.
 
System:
Gigabyte P35-DS4 rev2.1
Q6600 2.4GHz, 4GB G.Skill DDR2
2x Seagate Barracuda 7200.11 500GB as RAID1
Asus GeForce 8500GT 512MB GDDR3 PCIe
Antec Solo case, Nexus NX-8040 400W Silent PSU