A large number of people find the bass level is to low for their tastes after running Audyssey. These people will turn up the sub level on the AVR 2, 3, or more db to suit their preference. That is a fairly common thing to do.
When you change the Bass extension control on the sub, you are changing the FR of the sub. Audyssey tries to set filters to compensate for acoustic problems with your room. So, when you change the FR of the sub, you could be adding to a problem frequency in your room that Audyssey can't overcome, and you're hearing that as too much bass.
Set the Bass Extension to low, bump up the volume on the sub a little, run Audyssey. If you feel the bass is a bit low, bump it up a few db in the AVR so you are happy with it...and enjoy....
Just remember, it's your system, your room....Adjust it until you are happy with how it sounds....
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