in my experience and lots of others too, Audyssey sets the sub too weak for a flat perception; try boosting the sub level - in the avr - by 3 db. and make sure you use Dynamic EQ. and the right offsets for different sources.
this should give you a flat-to-the-ear perception of freq. resp.

if it still does not sound right, then you should review your Audyssey calibration and then see if there is a problem somewhere.

if you already do all this, then just delete my post. :-)

See: http://www.blu-ray.com/community/gallery.php?member=Gelli
or: Axiom Gallery