This does not happen when watching normal live television. Nor does it happen when I'm streaming Netflix through my ps3. We've had fios for about 6 months, prior to this we had comcast and I did NOT have this problem and I have the same audio setup. From the cable box I'm going via digital coaxial, I've also tried a optical cable, into my Mcintosh D100 DAC then into my McIntosh amplifier.
I did contact verizon a while back and was told to restart the modem and unplug everything for a minute which I did and the audio still flickers.