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FAQ
The disk drive numbers may not correspond as expected to the SATA channel numbers when you set up Windows Vista, Windows Server 2008, Windows Server 2008 R2, or Windows 7 on a computer that has multiple SATA or RAID disks.

Solution
The disk-assignment numbers may not necessarily match the corresponding SATA or RAID channel numbers. There is no assurance of a consistent relationship between PnP enumeration and the order of the hard disks that are detected during setup. Devices are presented in the order in which they are enumerated. Therefore, the disk-assignment numbers may change between startups. For example, assume that you run Windows Vista, Windows Server 2008, Windows Server 2008 R2, or Windows 7 Setup on a computer that has two unformatted SATA or RAID hard disks. In this situation, Windows may present the second hard disk as Disk 0 when you are prompted for the disk on which to install Windows Vista, Windows Server 2008, Windows Server 2008 R2, or Windows 7.

When you set up Windows Vista, Windows Server 2008, Windows Server 2008 R2, or Windows 7 on a computer that has multiple SATA or RAID hard disks, verify the disk drive on which you will set up Windows Vista, Windows Server 2008, Windows Server 2008 R2, or Windows 7 by checking the disk information. For example, on the screen that lets you select the drive for the setup destination, verify the volume name and the available space.

Note: You may not experience this problem when the Setup program runs on your computer. However, you may experience the problem if you configure Windows Vista, Windows Server 2008, Windows Server 2008 R2, or Windows 7 during installation or if you perform a recovery process that was provided by the computer manufacturer.

See below Microsoft's KB for more detail info:
http://support.microsoft.com/kb/937251/en-us
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