I can now hear the Sub, so I believe it's unlikely a fault. I am not sure why the YPAO has set it's volume to -7.5 when at that setting you can't really hear it, also if I am supposed to "fix it" by increasing the volume level at the Amp.
I'll try running the YPAO as discussed hopefully tonight, and see how I go.
Part of the issue is I am not sure how to tell if it's "right" I could hear bass last night, the upstairs was vibrating slightly when I had the volume up, so it's powerful enough, but it sounded a bit "boomy" to me.
Let's see what the recalibration shows.
when you run ypao, it is likely, for the sub (LFE) it gives out some cluster of freqencies, and there was one particular frequency that was quite likely your sub's strongest frequency, so it was in party mode when it produced it, which also happened to be your room's favourite frequency, got reflected by your walls/ceiling/floor combo and the mic picked up. it got confused. it wasn't happy. the algorithm said too much. so it turned it down.
ypao is not smart. it's dumb. it didn't account for your sub's quality, poor position, room acoustics. but it's better than you (or me), [but not a professional with a lot of equipment and a standalone DSP/EQ system, in addition to your amp]. i have a sony. after the EQ the bass is OFF THE CHARTS. everything is maxxxx bass. love it though lol. (but my room is an open room with no ability to reflect anything)
i'd like to think it does the best it can with the EQ hopefully that's where all the money in R&D was spent, but little things like your sub standing wave overkill and selecting the correct low pass filter setting, it wasn't R&D-ed into it. so you just fix it.
it's like if your phone has a setting out of the box that doesn't suit, just change it. no dramas.