Do you have a cable that is taking the audio output from your sound card to the audio input on your video card?
I had a friend that built a home theater PC and he had sound going through his HDMI, but it required all of these things:
1. Sound card with SPDIF output
2. SPDIF cable from the SPDIF output on the sound card to the SPDIF input on the video card
3. A video card that supported SPDIF input and HDMI output
I'm not sure if your situation is the same, but it may be similar. My friend's video card didn't receive the SPDIF signal through the PCIe slot.