Sorry, I misunderstood how you described your scenarios.
I think you have probably just gotten one of those weird scenarios where there is a hiccup in how the source device sends/encodes audio through HDMI. I have experienced this in other devices as well, and sometimes there isn't a good solution.
Is there a configuration you can modify in your software player? It could be trying to send 5.1 PCM or Dolby Digital over to the Onkyo receiver, but it is sending straight 2-channel PCM to the TV.
It's a strange problem for sure.