The FAQ may help:
f)5. Since I ran Audyssey everything sounds great - but where has my bass gone?
e)1. Is it OK to change the trim levels Audyssey sets?
Are you using Dynamic EQ? This will 'restore' your bass at low listening levels. What are your typical listening levels?
g)2. What is Dynamic EQ?
Thanks for the great information!
Where do I find the Dynamic EQ within my AVR?
I listen to mid volume level and I also listen to extremely loud or reference level for movies and music.
Dynamic EQ is in the Audyssey section of your menu, and (in Onkyos at least) is source dependent. What AVR do you have?