I had a "similar" problem a few months back, with slightly different symptoms. In my case bass management was applied inconsistently and incorrectly across various DSP settings

My unit had to be sent back to M for repair. Not sure what they did, but it works now.

DirecTV HR21, Ram modded Oppo 93, JRiver MC17 on Win7 wi/SSD, Empirical Audio Ultraclock Offramp, 861v6, Bryston 28B SST2 amps, Salk 12" Soundscapes with Dueland caps, RAM modded Audyssey Balanced Pro, Lumagen Radiance, MarantzS4