I’ve just realised that you have to use a Barlow lens with a DSLR dont you because of the back focus? In that case the 5.2 um pixel size entered in the general tab will definitely not be correct.
Looking at your screenshots Ha alpha is at 3383 and H beta at 1623 so the effective pixel size will be 1.774um which ties in with the 3x magnification factor quoted for the DSLR Barlow in the ALPY instruction manual. I suspect this is the main cause of the problem
Robin