Technically the thing that's causing the audio to drop out is your own digital receiver not the xbox... the receiver take a second to recognize the type of signal incoming before it begins decoding it.
When the Xbox is loading or changing scenes the Xbox stops outputting a digital signal... so when it starts again your receiver has to re-initialize. In an analog environment this doesn't matter at all, which is why your receiver doesn't have any problems, but a digital environment it makes a difference. Nothing is wrong with YOUR xbox, that's how they all work.
Imagine your digital audio receiver is like your car, and the engine revs are the sound output. Imagine loading screens are like traffic lights, the xbox has to stop and wait. but the Xbox 360 is stupid instead of letting the car idle, it drops the revs to complete 0 and stalls the car. When the light turns green the Xbox starts pushing on the gas to go but the car (your receiver) needs to start itself again because the Xbox was stupid and let the revs drop to zero... that's where the drop out comes from.
Forcing your receiver into Dolby Digital Mode instead of auto detecting is like forcing your car to stay running at the traffic light.
Cheap DVD players have this same behavior... any GOOD AV devices keeps a low level signal available to keep this from happening this can be fixed with software, so MS could do a dash update down the road and remedy the situation...
You'll notice on the Xbox 1 Games and the official DVD play don't have this problem but Xbox media center does... again it can be controlled with software.