Though IIRC you use a Yamaha unit with YPAO, which is different. The sub and speakers have an interchange in YPAO from what I've read. Audyssey the subs' level are handled separately unless the implementation in the 1400X is different from the three Audyssey avrs (two Denons and an Onkyo) that I use. Curious, tho, on your unit do speaker levels change if you manually change sub level after running YPAO?
@Borabis Now with the info about the speakers and placement in mind I don't understand the particular settings made, nor why they changed that much with one more run of Audyssey by only changing sub gain. Makes me wonder if Denon made some changes or there's something we're missing in how you ran Audyssey or if there's something wrong with the avr....
I've verified with my own units that sub level is set independently from speakers by wildly varying the starting sub level (which is manually set before the microphone run on all my Audyssey-equipped units), you set sub level to approx 75dB and you can vary it a bit depending on gain level on the sub. Speaker levels have not changed when I've done so...they work out fairly well along the lines of distance and the sensitivity of the speakers....