Ok boys, reran Audyssey through the app and all is good. I must have messed something up first time using the app. Levels are normal, set the subs both at 18 feet which is what I'm used to seeing. I had to go the normal adjustments of course, crossover, turn up subs. It set the subs to -8 which is normal, not +3. I bumped them to -3 of course.
I turned off midrange compensation, and limited the frequency to 400 hz. Oh I did all the Audyssey positions the correct way too. So I'm happy now. Thanks for the help guys.
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Good to know you seem to be getting good results with the $20 App. As always, following instructions to the letter is typically the best bet. It is also important to do it when you know the room will be quiet for the whole duration. Any sudden audible background noise such as a helicopter flying low will likely mess up the level.
It is also almost always better to leave the level settings and distance alone after running Audyssey, the mic is calibrated specifically for the job, you sound level meter likely won't have comparable accuracies for the purpose for various reasons. Also, as HD already explained, for active subwoofers, you can't good by the physical distance, Audyssey measured the delays so should be more accurate in most cases.
Bumping up the sub level for a few dB is a quick fix, but for better accuracy you can also customize the target curve easily so that it has a smoother curve tilting up to the left, such as the so called Harman's curve.
The notorious (to many people but some have no issues with it) flat curve is the main reason many Audyssey people prefer to turn it off altogether.
Dirac LIve and Anthem ARC seem to have their default curve more like "Harman's", Audyssey is still sticking to the "flat curve" that most don't prefer and the so called untrained listeners hate (remember ADTG, who would only use Audyssey with DEQ on when he was a Denon guy before he got converted..
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Below is from one of Dr. Toole's papers:
Subjectively preferred steady-state room curve targets in a typical... | Download Scientific Diagram (researchgate.net)