It finally came the time to upgrade my loved 990 to the 7701 and so far I am impressed. I do have an issue with the Audyssey set up. For some reason it is calibrating my Polk LSI 9 bookshelf speakers to Large. Any advice on why that is?

Audyssey attempts to determine if your speakers can handle low frequencies. If it senses that they can, it sets them to large and for many processors that bypasses the subwoofer by putting the lower frequencies to the mains. Go into the speaker settings and set the mains to small and then set the crossover frequency manually to somewhere around 80 hz depending on your mains. It shouldn't affect how Audyssey performs too much but it will let your sub do the heavy lifting and allow more power for your mains.

Thanks. I thought I read somewhere that any manual setting you make after running the Audyssey disables the Audyssey?

Audyssey will still keep its distance settings for all the speakers and does function remarkably well.