Hi
As usual, the very first step in troubleshooting a fix for this type of issue is to Uninstall and then reinstall the device. The ATA channel is actually controlled by the Southbridge chipset so if you have the disk that came with your MoBo, it's probably on there and you can try to reinstall it from that by inserting the disk when you get that second window again after rebooting.
If that doesn't do it, in Device Mgr and the properties of the ATA device, click "Uninstall" on the Drivers tab. Reboot and allow Windows to redetect and install the device if it can.
BIOS Flashes can be a tense time even for advanced users as ANY slight hiccup can make your computer an expensive paperweight. BOIS updates are ONLY recommended to resolve a problem that the BIOS update was written to resolve, or to add support for a new feature you need, other than that if it ain't broke...don't Flash it! Even the MoBo makers will tell you not to Flash unless they specifically tell you to in a support ticket, as many times with new BIOS updates some current features "can be" compromised in favor of a fix for something else and only They know which ones need flashing.
I would consider a BIOS flash to fix this as a Last Resort type of thing, and before doing it I would contact your MoBo support to see if they think it's going to fix or hurt you. I know many people flash their BIOS with every new update that comes out, and many times have no problems but all it takes is one failure.
