I had the same issue with new intel doggy bios, I revert it back to old version 54something and it works again so do not upgrade to any 55xx bios as per my exp...
I also having same issue with my new board DX58SO2 it is not picking intel controller as a primary controller.
I hope this helps.
I just upgraded to the latest bios (my last update was November '09); my setup is almost exactly the same as yours:
Win7 Ultimate 64-bit
4 Hard Drives
Disk 0: Velociraptor 300g(system install/boot drive)-Sata Port 2
Disk 1: Caviar Black 1TB#1 (Sata port 4)
Caviar Black 1TB #2 (Sata Port 5)
Caviar Green 2TB (Sata Port 6)
The latter 2 hard drives have suddenly gone missing from Windows altogether, although they're still detected in the bios setup. This is particularly worrisome since I just finished backing up all of my information to the 2TB disk in Port 6, and my primary storage disk is (you guessed it...) in Port 5.
I'm going to try to grab an earlier bios. If this doesn't work, I'll then start to panic.
DX58SO, Core i7 925, non-RAID setup.
Will update momentarily.
Clearly someone is not doing their job and not testing this stuff before pushing these updates out to the public. This is really shoddy from a company like Intel who I've supported for years and have always known to be very cautious of stability with bios update releases but that seems to not be the case anymore. I was considering installing 5529 after having major problems with 5506 but after reading this I'm staying away.
This seems to be the trend in the software world today, virtually every big software manufacturer I know of keeps pushing out bug riddled software and never seem able to fix the simplest of things and consumers are expected to spend their lives fiddling to fix problems created by some update or worse they are told to wait for the next version which promises great things which are never delivered.
I have the exact same problem; I can get the missing drive to re-appear by running Seatools but I really shouldn't have to. I've re-updated my BIOS, updated all of the board's drivers, run extensive tests on ALL of my hard drives but so far have not been able to get the drive to re-appear of its own accord.
Strangest of all is that before I run Seatools, I can't even see the drive under Disk Management in Windows 7's Management Console. Once I run Seatools, the drive appears as if I'd plugged in an external hard drive. Very odd.
Hopefully a new BIOS comes out soon that fixes the problem. If I stumble across a solution before then, I will post it here.
I suggest you log this case and get a case number. The more people that complain about problems with the latest BIOS releases for the DX58SO the better.
Click on Live Chat, chat to a consultant and ask them to create a case number for you. They'll do so and then email you a form to complete. Hopefully this then gets the info straight through to the engineers. Who knows?