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Based on the images supplied I would say you are trying to use flats that are not in exact alignment with the lights. If you remove the camera before taking flats then you will get the problem you have experienced. Peter (w) is correct using a pin alignment is the only way you can use flats from previous sessions or sessions afterwards.
I use a light box made up by EXFSO. If you can get the camera down to the same temp as the night of taking the flats then you can do flats at anytime with a light box so long as you don't have light leaks in you imaging system.
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