Don't know the Dish box very well. Was wondering if there's another digital option besides PCM/digital? Again, not knowing this unit well, I would only expect DD5.1 on the HD channels, although Dish does broadcast a few non HD programs with Dolby. "DD" is listed in the guide for the shows with 5.1 sound

With everything you've tried and everything suggested here, if you still have trouble it's time to swap components.

Exchange the Dish box first because a) it weighs less and b) the manufacturing is farmed out, probably to the lowest bidder, and is more likely to fail than the Yamaha product.