I am having the exact same issue - I have uninstalled the RealTek HD Audio and Intel Graphics Media Accelerator drivers and reinstalled and still the same thing - only the "SINGLE DISPLAY" option comes up in the configuration.
I was only using the HDMI output for audio. It cut out about 3 hours after working fine. No display options available now.
I had my Samsung LCD monitor on the DVI port, my desktop speakers on the regular speaker out configuration. In the graphics set-up I put the second monitor (HDMI) to CLONE and then was able to change my audio output from "RealTek HD" to "HDMI" - perfect, exactly as I wanted.
The Asus CS agent tells me that it shouldn't have worked like that and either the HDMI or the DVI can work, not both at the same time. So I could go VGA to the monitor and use HDMI for audio - but I can't get the options to come up so his only troubleshooting was whether I'd tried reinstalling the drivers, which I had already done.
Now my only option of moving forward is to send the mobo to ASUS...or I guess I could rerun a longer optical cable to my receiver instead of HDMI and limit myself to 24/96 stereo output as there are only certain files with higher sample rates...but eventually I want to use the PC in the HT room for video as well so I am kind of forced to send it in while it's still within the manufacturer's warranty.