Sorry for opening up an old thread, but need to throw in my two cents because I "had" the same problem and Gigabyte is slow to help.
Originally I had a DVI-HDMI cable and toslink cable from computer to my Denon 3808ci receiver, and then monitor to my Sony KDS-50A2020. Slow on the build, I never had a DVD player installed in the computer and assumed that the downloaded content that I was watching was standard def.
Then I installed a dvdrom and ran an HDMI cable to the receiver. To my surprise no Dolby Digital or DTS. As before, I was only able to passthrough 2 ch pcm. I reinstalled device drivers from Gigabyte and Realtek, no go.
Finally called Gigabyte and discovered the problem, or so I thought. Tech support insisted that I need to put in the driver CD and install Dolby Control Center. There ain't no Dolby Control Center on the Application menu. So we perused the cd and low and there was a folder named Dolby. I installed the 64 bit version, got off the phone and played a DVD. Guess what, still 2 ch pcm. Went into Dolby Control Center, chose the option for Digital Output S/PDIF and hooked the DVI-HDMI cable and toslink cable back up. and YAY! IT ALL WORKS!
One other werid thing I forgot to ask Tech support concerning the HD manager. It showed the HDMI as being installed with Microsoft drivers, device manager confirmed this. When I checked Digital Out, it showed Realtek.