Well nothing is perfect, how old are your QS8's. You can get an app for your smart phone and they are pretty accurate. I have a Iphone 4s and compared it to my calibrated sound meter and its as close as god is to damn , so plenty accurate enough to get all your speakers properly balanced. Let your room correction set the distances and then use your phone from your listening position to get them all set to the same db. I am not sure if the yamaha has a manual mode that outputs a sine wave but i think it would. If your fronts are louder than the rears lower the fronts rather than jacking the rears so you dont overdrive the preamp level and possible introduce distortion. Receivers have a preamp that drives the amp and if you get the levels set too high you may possible cause the preamp portion to clip.
Try putting a fan on your sub amp to see if its heat related. Subs take a lot of power when they are driven hard. IMHO if it takes 40 mins it is most likely heat related and or your subout on the the yamaha is set to high.
