Integrated image produces a swirl

That's an effect I've not really seen before. Can you tell me more about your setup and if there was any difference with shooting in Ha and SII? Are you dithering during data acquisition?

Hi, no difference in setup, data acquired using all three filters during same sessions over a period of a few weeks, same PHD2 small dither, etc. Deep Sky Stacker handles the exact same image and callibration set without issues  (basic stretch applied):

Ok, would you be able to upload a subset of all data (incl. calibration data) to our server for analysis?

Hi, data uploaded. Thanks

This is what I see post integration using the same:

Thank you, I'll have a better look

I noticed that the flats you provided have almost no signal, if you disable stretching it should have a nice signal at approx. 2/3 of the spectrum. Is that a mistake while uploading or actually the case? So I processed without flats or dark-flats. DSS has far simpler algorithms and that may have "helped" in this case, but they still wouldn't be correct flats.

This is the result I then get:

Little bit of post processing:

Thanks for going to the effort to check, I will review my calibration frames and run again, and let you know.