Don't know if this will help but...
I've got the 5805 and ran into a similar problem with the Audyssey set-up...after all the speakers did their thing, it kept getting hung-up on the subwoofer tones...retrying each one (I have 3) several times before finally give the error message "Room Ambiance Too Loud" or something like that. There was no "skip" option...the only thing it would let me do was "retry." Even though my room was graveyard quiet, I kept getting that error message no matter what I did. After crying, cursing and drinking I felt alot better, but the error message was still there. Turns out one of my sub's crossover filter wasn't set to bypass, and that flipped out the Audyssey program. It didn't tell me one of my subs was set-up wrong, it just said my room was too loud. After changing the setting on my sub, the set-up finished up without a hitch. It did tell me that my left rear surround was out of phase (which I ignored, because it wasn't) but there was a "skip" option to let me continue. As for your problem, all I can tell you is check your subwoofer settings to see if it's set to "bypass." Let me know what happens...