I am posting this as I am waiting for Windows x64 to install on the SATAII drive.
On a whim I decided to try the Silicon Image SATA ports that are on the motherboard. I did that, rebooted the computer, enabled the ports in BIOS, set the SI adapter to "Enabled" and made the driver disk. Went into Windows setup, loaded the drivers and we are good to go. I dont know if there is something wrong with the drivers or the ports or something for the nvraid ports because they are what the problem was.
Yay!