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Hi Pete,
Exposures shorter than ~1 sec will introduce shutter artifacts, but this might not be the problem you are seeing, the problem could be with the light box itself. The only good way to diagnose is to take some twilight/sky flats and compare. Point the scope near zenith about 10 deg in the direction away from the sun (e.g. a bit east at dusk). You will only need one flat to compare the light box result, but at least 7 frames, 11 preferred to make a good combined master flat (like you are doing). NB when making flats in twilight either turn tracking off of dither large amounts between frames, and try to stay out of the milky way...
Good luck,
EB
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