I'd need to know a little about your system, what center speaker do you have and what volume level do you listen at, to rule out your center channel speaker being the problem you could try switching a speaker around and plugging in your right or left speaker to the center channel and re-playing...
It could just be that you are used to bloated bass and when you get calibrated bass it sounds poor to you, my experience of YPAO, i own a Yamaha A1010, is that it never quite gets the subwoofer channel correct, it's actually closer if you run it three or four times but it never did it to my...