I kept thinking about this weird phenomenon and then something suddenly came to mind.
The app allows you to edit, but if you simply upload the file to the AVR after editing with the app, I am not sure if the changes would take effect. Remember I asked the question before about whether the app was actually doing the EQ or just editing. That was because the way you described how you have been using seemed to indicate the app would do the EQ as well. You may be 100% correct on this, but what if the app is really just an editor and it simply allows you to upload the edited target curve?
I know nothing about the app as I don't own the hardware and software, but I am guessing that if the app only does editing of the "target" curve, then the uploaded file may just be an edited target curve. It is therefore possible that you have to run Audyssey after the upload so that the AVR/Audyssey will try to follow the edited target curve when doing it thing this time, instead of the default target curve build in with the AVR.
Obviously all this is just my logical (hopefully) guess, thinking that you can set a new target, but you still have to take aim and pull the trigger again, otherwise the hole is still in the old target.
Of course all of the above would not explain why you were getting different high frequency response if you use (or thinking that you use) the app to do the EQ. I can't even guess how that happened, yet....
Also, please be aware that even if everything works, a 4 dB boost may not result in exactly 4 dB change in the exact place. The room effects will still be there, hopefully to a lesser degree. I know you mostly know that already, and I understand you are just aiming to get closer to perfection.