This maybe unrelated but,

I had a customer a month ago with a Yamaha AVR and DirecTV. System had worked fine for 3 years then he got an upgrade to the new DirecTV system.
Audio did the exact same thing you are saying, except it wouldn't come back on until you either rebooted the DTV receiver or went into the DTV menu and switched Dolby off then back on again. I determined it was a faulty DirecTV box and we just left Dolby turned off - he liked his surround sound in 5ch stereo anyway *facepalm*