Well every time you move the sub you really need to re-run YPAO. Moving a sub around to different spots using the same settings can give drastically different results. And you need to at least do a sub crawl before anything else, to determine the best one or two locations to place the sub for your main seating location. Then place the sub there and proceed. The flapping noise from the driver sounds like extreme excursion, which would likely mean the sub is being pushed too hard.
Game Room>Vivitek 1080p projector w/100" screen/ Hisense 65" 4K w/HDR10, Onkyo TX-NR656 receiver, Klipsch KF-28 L/R, KC-25 center, KB-15 sides, Loft 40 rears, RBH I-12/e (x2), I-12 (x2) subs. Living Room>Samsung 59" Plasma, Onkyo HT-R560 receiver, Primus P363 L/R, P163 center, Polk RC60i in-wall rears, SVS PB12-NSD (x2) subs. PC set up> Pioneer VSX-524, Pioneer BS22, SVS PC12-NSD (x2) subs. Game Systems> PS4, PS3, XBox One S, XBox One, XBox 360, Wii.