Okay... maybe it MIGHT just be for RAID but try enabling it and see if you can set the next setting to AHCI, if not then disable XHD and set the next for AHCI.
The SATA port numbering on this Gigabyte motherboard is confusing you. It has NOTHING to do with whether or not the drive is SATA I type or SATA II type. SATA I equals 1.5 Gbps and SATA II equals 3 Gbps. The port are backward compatible so that's not an issue. If your SATA drive is SATA II class then it will be recognized and run at 3 Gbps maximum "potential" speed.
Don't mess with the jumper settings at all on the hard drives. There are very few SATA III drives available at the moment (some call them SATA 6 because of the 6 Gbps transfer speed). Your Western Digital may be one of those that is 6 Gbps capable BUT your motherboard's P55 chipset only supports up to 3 Gbps SATA II hard drives.
Your motherboard's specs state that the Marvell chipset for ports 6 & 7 is 6 Gbps capable but I believe that's only in a RAID configuration, not a singe drive attachment.
Quote:
Intel P55 Chipset: - 6 x SATA 3Gb/s connectors (SATA2_0, SATA2_1, SATA2_2, SATA2_3, SATA2_4, SATA2_5) supporting up to 6 SATA 3Gb/s devices
- Support for SATA RAID 0, RAID 1, RAID 5, and RAID 10
Marvell 9128 chip: - 2 x SATA 6Gb/s connectors (GSATA3_6, GSATA3_7) supporting up to 2 SATA 6Gb/s devices
- Support for SATA RAID 0 and RAID 1
* SATA3 RAID 0 4x and SATA3 2x performance are maximum theoretical values. Actual performance may vary by system configuration.
* SATA3 SSDs are not recommended for use in RAID 0 mode on Marvell SE9128 ports.
JMB362 SATA2 chip: - 2 x eSATA 3Gb/s connectors on the back panel supporting up to 2 SATA 3Gb/s devices
- Support for SATA RAID 0, RAID 1, and JBOD
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You might call Gigabyte US Tech support and see what they tell you.
I own a Gigabyte motherboard and the only thing different about yours is the XHD feature, which confused me a little bit.
Try what I'm suggesting and see how it works out. The 6 SATA ports controlled by the Intel P55 chipset are the ones you want to use. Boot drive on port 0, the other hard drives on 1, 2, etc. I always put the DVD optical drive on the 6th port or port 5 as it's labeled on the motherboard.
READ your motherboard manual thoroughly in the BIOS section to be sure you understand what's going on there. I realize that most BIOS sections in motherboard manuals are not the most concise or explanatory of settings, configuration, etc., but the more you know what's available and how to set things the better off you'll be.
You might also try it the way that you were doing it, but don't hook up the other hard drive, just leave the WD hooked up to port 6 and set it as the primary boot hard drive. But be sure you set the DVD drive as the "First Boot Device" in the BIOS. Windows 7 is VERY FINICKY when it comes to having more than one hard drive connected during the initial install process.
Also you'll need to install the Marvell drivers in the initial install same as the Intel RST drivers are installed.