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I think I know what the problem might be, thanks for the suggestions. I believe the way I am taking flats might be from interference from the power supply used in my EL Panel I made years ago. It provides great light, but the electronics are very noisy. I will have to re-think my flats again.
The main reason I know is that I took some filtered images where I saw the same flat band on the lower section of the image only with a second band running through the middle. It has different colouring. The filter is a CLS filter. Thanks all.
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