This has nothing to do with windows. As a matter of fact, the only way you can get windows to recognize any devices on external mass storage controllers is by pressing F6 during setup or by specifying the driver path in oemdriverpath. Till the time SATA moves from PCI to Native, you are still gonna have this problem on most of the motherboards (except for the Intel mobos that have the ICH5 controllers, which in turn provide Native SATA support).
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