Again, forget about the auto calibration - it can severely mess things up. Just shut it off, grab your SPL meter, and do it manualy (sp?). Also, do not underestimate how much the location of the sub has on the sound. Play something that has a lot of repetitive bass. Walk around the room and you will find areas that have WAY too much bass, and others that have almost nill. Move the sub, and the location of these peak and null areas will change.
And as much as everyone says NOT to, if you're still not happy, set your mains to large, and set the sub crossover as low as it will go. That way, the sub is only reproducing the very lowest frequencies. Try it - you can always change it back.
