I know this post is almost a month old, but I thought I'd add my 2 cents. I have a Yamaha receiver as well, and was confused that the bass / treble / balance knobs didn't seem to have any effect on the sound. I found out that switching on "Pure Direct" bypasses all tone controls, sending the signal unchanged (but amplified) to the speakers.

I think most Yamaha folks know this, but it was news to me (I had to figure it out the hard way).