I agree it could possibly be the preamp section of the Yamaha. The best preamp section for music in an HT receiver would be one that has the ability to bypass most everthing but the volume control.
It might be too much trouble, but if this is the problem, a possibly cheap solution would be to pick up something like a passive Creek OBH-10 or OBH-12 and use it to listen to music, and then manually switch the cables back to the Yamaha for playing movies.
It might be too much trouble, but if this is the problem, a possibly cheap solution would be to pick up something like a passive Creek OBH-10 or OBH-12 and use it to listen to music, and then manually switch the cables back to the Yamaha for playing movies.