The Marvell 88SE9128 SATA 3 controller on  the X58 FTW3 also controls the IDE (PATA).  The SATA 3 controller has to be enabled to use the IDE header.  If it is disabled and the IDE drives can not be seen in windows re-enable the controller and the drives will be seen agian.  You can enable/disable the controller in the BIOS under Integrated Peripherals->Onboard PATA/SATA Devices-> SATA 3.0 Storage Controller.