I can't think of why that would happen either.
The Onboard Sata/Ide Controller works two separate SATA ports, aside from the usual 6 Intel SATA ports that come standard with the chipset.
Is it possible that you have your hard drive is plugged into one of the secondary Gigabyte SATA ports and not in the Intel ones? If so, that would mean that Windows was installed and is still running in IDE mode, since changing the Gigabyte controller to IDE will allow Windows to boot.
I believe that installing the SATA RAID/AHCI Driver is for the Intel chipset. And since it would not install I suspect it was installed already.
Anyway, you've got something unusual going on. I have both of my SATA controllers set to AHCI mode.