Sounds like there's some kind of signal dropout occurring. It happens on occasion with my Yamaha as well (most typically during layer transitions on DVDs), but nowhere near as frequently as you're saying. First thing I would try is go to the setup menu and have the auto mode detect set to automatically default to the last format used so that it doesn't constantly hunt for a change in sound format. The type of dropout you're noting might be the receiver thinking that the signal format has changed when it detects any momentary signal interruption.

The unit's still under warranty, so you might want to contact Yamaha and see if they've identified any problems with the new processor chip in that receiver since your receiver's the first model that uses that design. Otherwise, try a different digital cable first and see if things improve.