This is chipset limitation. ICH9 embedded two EHCI Host Controllers and six UHCI Host Controllers, supporting up to twelve USB ports. When USB 2.0 controller is set disabled , EHCI #2EHCI Host Controllersand UHCI#4 ,UHCI#5 ,UHCI#6UHCI Host Controllers are not available. Therefore, rear USB ports are not available and only front USB ports are available.
According to the chipset specification of GSATA2Sili5723, if you want to use a single SATA HDD without RAID 1 Smart Backup feature on this motherboard, please connect the SATA HDD to GS-0 Source or GS-2 Source GSATA2 port only.
After you connect the HDD properly, please go to [Integrated Peripherals] submenu in the BIOS, then adjust the [Smart Backup Function] option to all or you can just choose the corresponding GS-source you are using on the motherboard. In addition, please enable the [Smart Backup Initial] option then test again. Please do not forget to save the changes before you exit the BIOS Setup.