I've just setup a new PC and have installed 64-bit Linux with the plan being to setup XP 32-bit & Vista 64-bit as virtual OS's. In the BIOS I selected AHCI mode because I read somewhere that this was the way to go and assume that there are performance benefits through things like Native Command Queuing etc. Before I go any further does anyone know of obvious reasons why using AHCI mode should be a problem?
From what i've heard you will end up having to reinstall windows to make use of the extra stuff, however I have no idea if that applies to linux as well.
There are ways round that if you have an ICH8R or ICH9R southbridge. For me, the possible advantages didn't seem worth the messing (and risks).
Not really a problem in my case as this was a new build so nothing was installed, as you say the risk could be switching to AHCI afterwards.
Using AHCI made my 2k8 install take ~15s longer to boot.. but that could just be the mobo I was using.