P5GD2 Premium IDE/SATA AHCI help?

Looking for some advice on what might be wrong here. New build in process.
Never started from scratch before so bear with me please.

ASUS P5GD2 Premium
Intel 540J CPU
1Gig Corsair Ram
Lite-On SOHC-5235k Combo drive on Primary IDE as master(tried sec also)
120G Seagate SATA HD w/ NCQ on the ICH6R controller
2 more SATA Seagate drives to follow at later date.
No RAID. No plans for RAID in future.

Under the IDE Configuration in the bios (1009) I started with the 'Configure
SATA As' at the default of 'Standard IDE'. Installed WinXP Pro, using F6
method to install ICH6R drivers. All works fine. XP up and running.
Changed 'Configure SATA As' to 'AHCI' knowing that a re-install of OS would
be needed.
Here's the problem- The CD drive no longer will boot from the Windows
Install disk correctly. Drive spins up, then nothing. Later screen shows
'Setup is inspecting your....Normally XP install start. Then everything
seems to hang, just a black screen. However a DOS Boot CD will start just
fine. So the drive is working.

Have I missed a step? Is AHCI the problem? Do I benefit from AHCI where I
would miss it if it wasn't there?

Thanks in advance.