I think something similar has happen to me in the past (master FLAT not applied whileI was under the impression it was); e.g. see issue reported in the first posting in the thread https://www.starry-night.nl/forums/topic/m3-bolhoop.
So do I got it right when I follow the following flow for mono-subs using color filters?
1) Create master BIAS (app. 100 -250 subs), clear all frames
2) Create master DARK (app. 50 subs) while loading master BIAS as well, clear all frames
3) Create master FLAT (app. 50 subs) while loading master BIAS and master DARK, clear all frames
4) Create Bad Pixel Map while loader master BIAS, master DARK and master FLAT
5) Calibrate subs while loading, Bad Pixel Map master BIAS, master DARK and master FLAT, clear all frames
6a) For additional colour subs only: Load reference frame and perform star analyses on all frames and unselect reference frame and select it under Registration as reference frame
6b) For first colour subs only: perform Star Analyses and remember selected reference frame
7) Select Windsor Clipping in Integrate and press Stack to Register, Normalise and Integrate frames of this colour
8) Repeat step 3, 4, 5, 6 and 7 for each color filter applied
9) When needed correct light pollution, vignetting and combine colours to a single RGB stack
10) Optimise photo using preferred tooling…
Let me know if I understood it correctly and if not, where I go wrong…