S/PDIF supports 5.1 channel sound, so I doubt it's the motherboard. However, not all DVDs are created equally, meaning each DVD could support between 1 and 6 channels. I'd try a DVD that you know supports Dolby 5.1 and see if it is fully utilized. If not then I'd start checking the connections and settings.
I recently put together a media computer. The mother board has an optical output for audio that I ran to my receiver hoping I could get Dolby 5.1 out of it. The problem is I only seem to be getting 2 channel audio out of the computer. Is this a limitaion of the audio on the motherboard or is it a limitation of how the DVD is read by the computer? Thanks,