We had FiOS set up about 3 weeks ago now with the VMS 1100 also. I've noticed the intermittent but frequent drop outs also. It's very short, maybe even less than a second. I could almost believe I imagined it if it didn't occur so frequently.
It's interesting that you mention Yamaha. I have the tv connected by optical cable to a Yamaha sound bar and the DVR connected to my Sony tv by HDMI. I also have an Apple TV connected to the tv but never notice any audio issues with the Yamaha. It seems to occur more so with certain networks. So it may be more of a network issue than a local equipment issue.