Those ports uses a different AHCI driver. You need to reinstall the AHCI driver, or use a trick like this:
http://forum.corsair.com/forums/showthread.php?t=94426
So switch it to the SATA 2 port (slower port), boot into windows, switch the registry (see the link, or use the script) to use the generic driver, then plug the drive into the SATA 3 port (faster port) and boot windows.
Here is the Micro$haft instructions (assuming the drive is bootable, so plug it back to the other port first):
"To resolve this issue yourself, enable the AHCI driver in the registry before you change the SATA mode of the boot drive. To do this, follow these steps:
Exit all Windows-based programs.
Click Start, type regedit in the Start Search box, and then press ENTER.
If you receive the User Account Control dialog box, click Continue.
Locate and then click one of the following registry subkeys:
HKEY_LOCAL_MACHINE\System\CurrentControlSet\Services\Msahci
HKEY_LOCAL_MACHINE\System\CurrentControlSet\Services\IastorV
In the pane on the right side, right-click Start in the Name column, and then click Modify.
In the Value data box, type 0, and then click OK.
On the File menu, click Exit to close Registry Editor.
"
Then plug it into the faster SATA port.