Let me try one more time, I think it could be that we both got caught in semantics!
Before you spent time on any tweaking to prove me right or wrong, please re-read my post#79 as I don't really want you to waste your time on something I said. Think about this, if you have a sub that is much more sensitive than your speakers, and you turn it's volume way up because you like super hot bass. Now you run Audyssey, don't you think Audyssey will have to raise the levels of the other speakers to match the level of the sub? For my AV8801, the lowest level Audyssey can set my sub to is -12 dB, can't go lower than that. Another point, you have been referring to Audyssey, the OP has YPAO, that may have even less range for the sub level and if so, it will logically be more "dependent" on the sub's volume knob position, but that should be a question for Yamaha. However, the OP did say (twice), that if you turn the sub off, YPAO would then set the speaker levels lower, to what he expected to see so that sort of reinforce of what I believe may be happening, in his set up.
Again, I agree it is time to take it private, if needed..