Room correction is an awesome thing but it's not perfect.
One thing that I've found is that if you have a big null, it's ok to make it go away by changing different sub position/phase settings, within reason, but it's a terrible idea to make it go away by filling in the hole, even if you have enough power and eq to do so. The room eq is not always smart enough to know this, particularly with some of these high output systems.
The fix, so far for me, has been to get a decent average freq response and make the target curve somewhat follow if there are nulls. I.e. I have a 70hz suckout on one of my systems and enough horsepower to fill it, but it sounds absolutely terrible if I do, as it's an enormous eq peak and the whole room outside that listening position has some serious reverb issues... sounds much better to just jog down on target response 5dB or so right in the area of the null. This is harder to do with Audyssey but you can always do after with a minidsp, the room modes aren't going to change.