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I would not be adjusting colour before stacking. Wrong sequence. Stack then adjust for colour. You probably are saturating light pollution (its usually greenish). Also it looks like your flats are not flattening the image properly.
What is your procedure for doing flats? I have found that flats are more important in light polluted areas than in dark skies.
Another aid is the free HALVG plug for Photoshop from Andrea Rogelio that removes excess green from images. It would correct a lot of that.
Greg.
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