I find with my CMOS cameras that careful calibration is a must, more so than with a CCD, or this sort of fixed pattern noise bleeds through. I also find that CMOS Darks don't optimise too well so same duration and temperature and turn off optimisation in calibration. At that focal length I am also guessing you are operating at quite a slow focal ratio so 3 minute subs in Ha is on the short side. Crazy as it sounds, 47 x 3 minutes is also on the lower end for Ha. You still have only just over 2 hours of integration time. I aim for 100+ of that sort of duration and that is at f5. I have done a couple of targets with 180 dithered subs and the results are very noise free.
Chris