Two things to try;
1 Run the R820s as they are now located but by themselves without the rest of your HT speakers or the Audyssey.
2 Move the R820s well out of the corners and play them without using the Audyssey - play them full range and uncorrected.
If either of these things changes the sound for the better, you've got a starting point. If not you can cross an easy thing off the list.
My thought on your set up is that you have rear ported speakers that can sound boomy when too close to boundaries, pushed into corners. The correction software may decrease the bass to compensate for the added and muffled bass from the corner location. I have a pair of RP280s that I had to move out from the rear and side walls about 3ft each way (to the front of the baffle) to get the bass to sound relatively flat. When they were closer to the walls the bass was of the one note type and the closer to the walls they were, the boomier they got. They sound pretty good now.