Which receiver are you using?

When you do the audyssey setup are you doing 3,4, or more locations? I have found Audyssey really needs the extra locations to get its EQ right.

Do you have the latest firmware updates for your receiver, if avaialble? There could be other noises that are causing Audyssey to set things up wrong, make sure the room is dead quiet. I do my set ups at 2-3AM when I get home from work.

Jason
M80 v2
VP160 v3
QS8 v2
PB13 Ultra
Denon 3808
Samsung 85" Q70