My new Gigabyte GA-Z87X-D3H main board was working fine at first, before I installed Windows 8. The main board was recognising the 3 attached hard drives and CD drive fine.
However, during the Windows 8 install I noticed that the installer program was interpreting the 3 hard drives all as 'Drive 0' and simply naming them as different partitions (Drive 0 Partition 1, Drive 0 Partition 2, Drive 0 Partition 3). I proceeded with the install and noticed that only 'Drive 0' - my main drive - was formatted, as I would expect.
However, since then Windows does not recognise any other connected Drives except the CD Drive and the Drive on which it is installed. What's even MORE worrying is that now my Main Board's BIOS doesn't recognise the other 2 HDDs either, whereas before it was detecting them fine.
I have changed the BIOS' SATA mode from AHCI to IDE, at which point it DOES recognise the other drives, but then Windows BSODs when I try to boot up so I have to switch back to AHCI to get Windows to boot.
I discovered the cause of the problem. It seems the GA-Z87-D3H has two BIOS modes. The '3D' mode and the 'Classic Mode'. Classic Mode can be selected from the menu on the middle-right side of the screen. A SATA port can be Enabled in the 3D mode, but if it isn't also Enabled in the 'Classic' BIOS then the port is still considered Disabled.
I solved the issue by enabling all my SATA ports in both '3D' and 'Classic' BIOS modes.