OK, if you ran with the sub on you will need to go thru the receiver setup to the "Levels" section and scroll thru until you find "SUB". You will notice that YPAO will turn sub level almost all the way down. Re-adjust the sub level to whatever you like, half signal or whatever. If your sub is super efficient it will do that or in your case super awesome.
Running YPAO without sub: You will need to go to the "Configure" section within "Setup" and you will see that "Bass" will be set to "Fronts". Your choices should be SWR, Front, or Both. Re-set "BASS" to "SWR" and re-plug in your signal cable and should be good to go with however your subs were calibrated.