Hey Rick, thanks for your help. I figured it all out. After doing it with Staralign and working on the debeyered images (I thought I was taking the output from the calibration step in BPP, turns out the output was actually in a subfolder called debeyered...) it still failed on 10 images.
When the calibration step was done, the overscan portions of the image was different in each picture. On the long exposure image the overscan area is brighter. Example attached.
I didn't know the significance of it but I batch cropped all the overscan areas out and now I managed to get 100% of the images to stack.
Thanks a lot for your help.
