While this doesn't apply to all setups I found adding an optical cable from the HDTV back to the HTS often fixes the missing audio.
Hi CNET! This "how to" is just in time. I recently got a new HTS and connected it to my HDTV and 3D blu-ray player. However, I cannot hear TV sound through my speakers. I can get sound from the speakers as long as my blu-ray player is on, but I can't get surround sound from the TV. My goal is to be able to hear surround sound through the TV as well as the blu-ray player. Right now, I only get it from the Blu-ray player. Before I call the Geek Squad to help, I want to exhaust all other methods. I appreciate whatever help you can offer. Thanks!