How did you establish the proper level of the sub? Test tones? SPL meter? At least I don't think Denons that old had an auto setup or Audyssey feature.
If you turned off the THX switch I mentioned the sub's low pass filter should be turned off (it's only half a crossover as such, since there's no corresponding high pass filter in the sub). You should set crossovers in the avr....I'd start with 80 generally (be sure to set speakers to "small").
Your perception of sound and frequency varies with level. Don't know if your Denon has a loudness contour type setting, but try this article for the concept
https://en.wikipedia.org/wiki/Equal-loudness_contour
If your sub doesn't have stronger bass in either of the phase settings then there's not much you can do (you generally use the setting that yields the stronger response).