Hey man, I was having the same problem with my earthquake supernova mkV 10" , had it hooked up with a Y conector and was getting distortion with audyssey during the Iron Man cave scene. I got rid of the y connector and that got rid of almost all the distortion while using the audyssey EQ. I dont know if this is a fix for my specific sub but it made a big difference. also by doing this I was able to raise the volume on the sub getting the subs amplifier to do more work and have more control over the it. Woth a try if you have it wired up that way. 
Ive got a vid of the sub before I got rid of the Y conector.
http://www.youtube.com/watch?v=Ui6o9sCiMxU
Hope this helps.
Ive got a vid of the sub before I got rid of the Y conector.http://www.youtube.com/watch?v=Ui6o9sCiMxU
Hope this helps.
