A recent discovery I made because of my mobo's odd controller:
While its true that AHCI works out of the box with Vista/Windows 7 (that is, there is no need for third party drivers) -- If you did not have it enabled when you first install Windows, it will be disabled to save some boot time. Makes sense. What's odd is what you have to do to enable it. You have to change HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\services\msahci\Start from 0x3 to 0x0. Otherwise, you get a blue screen when you try to boot. The fancy startup repair that comes with Vista/Windows 7 will be launched the next boot (if you let it), but won't be able to figure this out for you.
So yea, I tried moving the cables around on the inside (thinking it might be a bad sata port), and changed to AHCI, and my cd drive was still the one that disappeared, not the drive in that port. I thought it might be some incompatibility with the firmware, but the updater fails to run. :'( I suppose it's also possible it's a bad cable.