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Pete,
Make sure you've got everything checked in MaximDL as per the attached.
In particular if your scaling your darks, click on the dark frame group to determine what scaling you are doing. auto-scale is the conventional method, auto-optimize is RMS noise based similar to that used in CCDStack. You may find you'll obtain a better result with the latter - experiment. I typically build the bias and dark frame masters before processing the flats.
Looking at the images in post 28, your flats are over correcting the light frames hence the reason why you have a dark band down the center. You need to ensure your flats are accurate as possible. Ideally, what you should be left with is no system characteristics, i.e. donuts and huge gradient shifts, but more the typical sky glow and smoother gradients caused by light pollution. Looking at the raw light frame and the flat, I would suggest the flat isn't matching the system characteristics.
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