Disks Missing in Action

Specs:

C2Q 6600
Gigabyte GA-X38-DQ6 (BIOS F6b)
OCZ GameXstrem 850w PSU
8gb OCZ PC2-6400
Gainward Geforce 8800 Ultra
X-fi Elite Pro
4x WD 1TB Drives
2x DVD-RW

I have the SATA drives plugged into the Orange ICH9R sockets and the OPticals plugged into the Blue sockets.

When the PC boots, the BIOS finds 2 drives at 900 odd GB and 2 at 0gb. Windows offers to format the 0gb drives as 30mb partitions. I booted using a Linux Live DVD and when I restarted the other 2 disks came in at the 900 odd gb. They stayed online until the next restart when they returned to 0gb.

Im fairly sure I have enough power, and I tried moving the drives to the purple gigabyte SATA sockets but I am puzzled as to why 2 drives are not appearing

I would try booting with only your system disk connected, remove the sata cable for all the other drives before booting the computer.

SATA drives are hot-pluggable, you can connect them once the system is running, so once the system is booted with just your system disk on, hot-plug a SATA cable in to one of the other drives and wait for it to come up in windows, check all is ok with it, then hot plug another.

Do all the drives come up ok using this method ? or do you still get the same problem ?

If you get the same problem, repeat the process, but hot plug them in a different order this time to see if it's only the last drives connected that suffer this, or if it's physically the same drives that do it each time...

It's possible your drives may need a firmware flash, or your motherboard may need a BIOS update, just guessing at this stage, try the above first and see what happens.