I am having this same issue due to a virus recovery process. I have an Intel D975XBX2 motherboard, which has Intel IC7 southbridge and a secondary Marvell 61xxx chipset. I am using the Intel IC7 ports with 4 drives in RAID0 for video/audio data workspace. I have 2 - 500GB drives on the Marvel ports for OS and other data drive, both using the AHCI mode. The Marvell 61xxx BIOS control is basically ON or OFF, and requires the RAID capable drivers.
The deal is I had dual boot with XP for years, but never really used it this way, when I udpated from XP to Win7. The older data drive is actually my older WinXP drive. When recovering from a virus, I had each drive out in a USB box on another machine and did a cleanup on the WinXP older drive, forgetting that the dual boot setup actually has the boot sector on that older drive. No matter, I only want Win7 going forward. I put the Win7 drive on the Intel IC7 ports with them in IDE mode and was able to use the repair console for add a bootmgr onto the Win7 drive. However, I have not been able to get this drive to support the Marvell ports for boot up. I checked the registry and the drivers list and the up to date Marvell drivers are already installed and the start mode is set to 0 in the registry, HKEY_LOCAL_MACHINE\System\CurrentControlSet\Services\Marvell Startup = 0 (which should mean this driver is available at boot time).
But, it still doesn't work. I have this machine currently setup with these two standalone drives on the Intel IC7 in IDE mode. I want to get them back onto the Marvell ports so I can recover my RAID 0 2TB partition and get back to work... Any ideas?