A couple of questions:-
Is there any peformance penalty using the AHCI BIOS?
AHCI is a VERY well published standard by INtel, and from what I've read, AHCI is the preferred mode if you're rtunning in native SATA mode.
I've beren running a MythTV box with software raid 1 using AHCI mode with no problems at all for the past year.
HTH
Chris