To William's point:
Use this calculator to see what you room modes are!
HTML5 room mode calculator. Read and hear the tune of axial, tangential and oblique modes. Scientific sources included.
amcoustics.com
If it is square or close to square, that means the same (or close) frequency could be resonating in both the length and width dimension which means you might have a rater extreme resonance that exceeds Audyssey's capabilities!
As a quick (free) check, you can run the 10Hz - 200Hz test sweep at this link through your system:
A frequency sweep from 10 Hz up to 200 Hz.
www.audiocheck.net
Turn the volume low as you don't want to send really strong, really low frequencies through your system at high volume. Listen to see if tone at or near the pitches identified by the mode calculator (or any tones, for that matter) are
obviously louder than the other pitches. If so, you are probably experiencing what William suggested and it would be money well spent to get the miniDSP and a umik-1 with REW software so you can tune your system.
Edit - it wouldn't hurt to do the Sub Crawl to see if that resolves the issue before buying the miniDSP!