Problems when switching BIOS settings to AHCI; two of my drives vanish

Win7-64 Home Premium SP1
mobo: Gigabyte EX58-UD3R (latest possible Firmware)

hard drives:
* physical 1: 500GB WD AAKS, for C: and D:
* physical 2: 1 TB WD, split into two partitions
* physical 3: 500GB WD, drive G: ... for storage
* physical 4: 500GB WD AAKS: drive K: for steam/games
* physical 5: 3 TB WD green, in an external dock (Thermaltake BlacX)

* (soon: Crucial M500 240GB SSD)

I have a new 240 GB SSD on order, and I've been reading that I need to enable AHCI in the BIOS to get the most out of it - if not to get it to work at all (my buddy said his wouldn't work until AHCI was enabled)

So I did the registry edit MS published that lets you enable AHCI on an existing windows installation. Then I go to the BIOS, and changed two settings to AHCI. Here are the screens of my BIOS, and what I see:

imgur: the simple image sharer

One entry is "ICH SATA control mode", and the other is "Onboard SATA/IDE control mode"

Both have options to change to AHCI. I have no idea why there are two different ones, or what either means. I changed both. I rebooted and the PC goes through an AHCI search function during the boot. It gets to windows and windows goes through a lengthy process of installing drivers, which seemed to be successful, but the problem is that when I now go into Device Mgr, I get errors on two of my ATA channels under "IDE ATA/ATAPI controllers" -- I get exclamation points by two of the ATA channels. And sure enough, two of my physical drives have vanished from Windows Explorer -- always physical drives 3 and 4 (drives G: and K:)

When I get the SSD, is it best just to install Windows clean? I'd prefer to clone my existing C: to it, but if I install clean - should that resolve the AHCI issue? Or is there something I can do now to resolve it? or should I just forget about AHCI, and go back to IDE in the BIOS?

Thanks a bunch for reading this and for any help.

Are all of your drives SATA drives?

What happens if you change the "Onboard SATA/IDE Control Mode" only?
What happens is you change the "ICH SATA Control Mode" only?

TVeblen said:

Are all of your drives SATA drives?

Yes.

TVeblen said:

What happens if you change the "Onboard SATA/IDE Control Mode" only?
What happens is you change the "ICH SATA Control Mode" only?

If I toggle either of those, some of the drives that do show up (with both enabled), aren't found and disappear.

Damned strange.
What motherboard are you using, or if pre-built, what is the brand and model number?

EDIT: I see MB in first post, sorry.
Do all the drives show up in BIOS? Or is the problem just in Windows?

Are all the drives plugged into only the BLUE SATA ports?
Do you have any drives plugged into the WHITE SATA ports?
Are you using any IDE Drives in the IDE port?