I still feel like it's somehow related to the flip. The dusts appears to have moved very slightly between frames 10 and 50 and I suspect it's during the flip.
Can you try to do a WBPP run with the frames from one side of the meridian only (the side where you took your flats)?
Another strange thing is that there is a diagonal gradient on your calibrated frames 10 and 50 but the gradient is the same on both frames (darker in the bottom left corner, brighter in the top right corner). If this was due to a gradient in the sky I would expect it to be rotated 180° between the two images so I assume this indicates a problem with your flats.