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Pete try 'correcting' a single flat with your master flat. If the result is uniform in brightness that means the software is not at fault.
Any uneven illumination from an artificial light source will show up in a flat corrected real astro image.
I have personally tried every method for flats and have found that blue sky flats taken with darks beats any other method. Of course this assumes your camera can take very short exposures. My Canon 5DH can and they are typically at 1/320th sec at an ISO of 200 at late afternoon when the observatory is in shade from direct Sun.
Bert
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