The reason I suggested trying full range was the 15dB rise in LF coupled with your cotton stuffed in the ear comment.I played with this for quite some time. I turned the subs off through the Marantz, and ran he fronts in full range. If I have the Audyssey MultiEQ set to L/R bypass it sounds best. As I remember it used to be.
Your observation suggests the issue is with the subs, either level, calibration, or integration with mains. The easiest thing to try at this point might be to re-run Audyssey, being sure shakers are off, of course.