In your mobo's BIOS Setup screens look in the Integrated Peripherals screens. Besides the choice of RAID or SATA, is there a place specifically to enable or disable the SATA disk controllers and ports? Maybe when you flashed to the new BIOS version it set them all Disbaled by default.
I couldn't find ANY settings in the bios other than to choose between Raid and SATA, there was a sub menu under 'RAID' to enable or disable 'BootROM Function' which didn't seem to do anything either.
Also, the reason I flashed to the new BIOS was to hopefully GET some more options to make it work. I really think there should be some kind of 'controller card' like sub bios menu that shows up after the normal BIOS completes. Anyway, maybe it just never worked in the first place.