There are some previous posts on this topic, but the bottom line is the auto setup feature of the 990 works well for some and not so well for others. My suggestion is to invest in a Radio Shack SPL meter and set up the 990 manually if the 990's auto setup consistently gives odd results. I have noticed the 990 held most settings when I ran the auto setup after manually setting the crossovers, delay and level. The only one it tried to change was the subwoofer setting. I've not had a problem with a popping sub during setup. How loud was the pop in comparison to the test tones?