I experience such a problem like this also with my GA-P35-DS4 and WIndows XP, but this was an issue with Gigabyte's driver disc, it contained the wrong driver for the ICH9

What's a bit weird: Windows Vista comes with support for ICH9/ICH9R due to the fact that I don't needed an additional driver when installed Vista (x64 Home Premium) on my ICH9R based RAID5

(probably there's support for RAID and none for AHCI). So I think it possibly is (or was) a configuration problem in the BIOS.
Just to ask (if it is still not running): After the BIOS Post from the board itselfs, there's also a post and listing from the Intel AHCI BIOS, are the drives listed there correctly ?