"To enable hot plug capability for the SATA connectors (SATAII0, SATAII1, SATAII4, SATAII5) controlled by the ICH9 South Bridge, you must install Windows Vista (on ICH9, hot plug is supported in Windows Vista only) and configure the SATA connectors for AHCI mode. The requirements above do not apply to the SATA connectors (GSATAII0, GSATAII1) controlled by the GIGABYTE SATA2 controller. (Refer to Chapter 2, "BIOS Setup," "Integrated Peripherals," for details on enabling AHCI.)"
If you get oddball behavior then one simple fix is to move the effected drive's ports; e.g. 1->2, 2->3, 3->1 restart -- and if you want then move them all back - this forces Windows to rewrite registry and driver values which 'can' get easily corrupted going IDE->AHCI.