The sub isn't sounding thin. What happens is that I get better sound from the mains when I play music with no sub in "Stereo direct" mode (which plyas with no sub).

I've been playing most music in Stereo direct mode but I do change it to 2 channel stereo (which includes sub) for raggae and the likes.

I believe the "direct" mode on your Denon is called "straight" on the Yamaha FWIW.