Not sure what range of frequencies you're trying to describe, whether you're missing low bass or mid-bass.
If you set up a crossovers and levels I'm assuming you used the AccuEQ/Auto Speaker Setup program (but nice if you would confirm such) and have bass management on (i.e. your speakers set to small/use crossover, i.e. not full band) but some avrs may display a crossover suggested from the auto setup and still be set to large/full band. Look at page 39 of
the manual.
It is hard to guess at what other settings/sound modes you may be using without details, too.