OK. The HDMI cable from the DVR to the TV should not affect anything. It is used to feed video to the TV. (The HDMI audio output could also drive the TV speakers if you didn't want to use the sound system. But, that's not what is happening here.)
So, what about the questions I asked re: the optical cable from the TV to the receiver? That's the next step in this process.
btw, the DVR and TV have optical OUTPUTS. The receiver has optical INPUTS. And to avoid confusion about your devices, please refer to the actual equipment rather than talking about sound from "TV programs". In other words, when you select a show on the Direct TV set top box, you get audio from the receiver speakers. But, when you use Netflix on the television set, you get audio from the TV speakers and not from the receiver speakers.