The most likely reason for this is that the AVR maker insists on setting speakers to Large when there is a subwoofer in the system. Audyssey does not make this setting. In fact, Audyssey strongly recommends that if you have a subwoofer then all speakers must be set to Small for best performance. The MultEQ filters in the subwoofer channel have 8x more resolution than the other channels and this gives you a much smoother bass response. If some speakers have been set to Large then no bass at all is being sent to the subwoofer from those speakers.
Please also make sure you look here for the proper subwoofer settings to make sure they are not interfering with the measurements:
And finally, take a look at the diagram here for proper mic placement. Many times we see people placing the mic off axis (outside the spacing of the front speakers) and this can cause unneeded high frequency boost. Also avoid placing the mic too close to the back wall where all the bass buildup can cause the filters to cut the bass more than needed: