Actually now you come to mention it, i think i had a similar problem when installing Win7 7k on my R0 w/AHCI. In the end i made a boot disk with Vlite and slipped in the Intel ICH9R drivers and the latest matrix manager in the apps.
The only other thing i remember doing different was not formatting/deleting partitions or owt on the array i just let windows sort it out for itself, worked a charm.
i'll be home tomorrow night if you still need it looked at.