<snip....I have ....Integra DTC-9.8 with Audyssey.
Bingo. That right there is your problem. I have the 9.8 also. I tried Audyssey calibration with the supplied mic and what I heard coming out of my system sounded exactly like how your graph reads. Go back into the 9.8 settings and defeat the EQing completely. Set everything to flat. When you do that your speakers will come back to life, mine did.