I also am having trouble stacking h-alpha. I can get 5 to stack, but if I stack 10, they do not align correctly. I tried every setting I can think of in Affinity. Here is a solution that poster "Skylab" found, in the cloudynights forum:
"This seems to be quite common. I have troubles stacking my Ha images in PixInsight too.
At least in my case, the reason is that the strong noise in the green and blue channels (where there is almost no signal) interferes with the star-detection algorithm and leads to failures in registration. (This seems to be your problem too, at least part of it.) What I did to solve this is to ask PixInsight to use the super-pixel mode to deBayer, and then to extract the red channel of the deBayered color image. The resultant gray-scale images stack very well. This works because in the super-pixel mode, whatever in the green and blue will not contaminate the red. (Bilinear deBayering should also have this property, but I did not try it.)"
Attached is a screenshot of my attempt at stacking ten raw files. BTW the OIII and non-filtered stacked fine.
This makes sense to me, but I don't know if Affinity can extract the red channel and dismiss the others? -Noah Frere