I am having the same problem with my new FIOS TVOne unit. My mini TVOne box is connected to the Samsung Q7CnTV with HDMI and the TV is connected to the Polk Audio surroundbar 5000 with an Optical cable.
I get sound from the soundbar at the time of the Quantum TV setup and it sounds wonderful, but no sound from the new Media Server DVR after I set up the set-top box connection. FIOS works through the TV speakers. Another strange thing is that the soundbar works with Youtube through the smart hub app.
Please help!!!!
(FYI - My old verizon DVR box works with the soundbar using the same connections).