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Read your post again.
Ah! You can't take 1 second exposures for flats with a shuttered camera. The flat will pick up part of the shutter.
I found 3 seconds was about the minimum exposure for flats. Although when I did get shutter effects they didn't look like that.
Also you flat box seems way too bright. Those shots would make bad flats as they are badly overexposed. See if you can turn down the light box a lot and try 4 second exposures and keep turning it down until you get about 25,000ADU for a flat with no badly overexposed areas.
Its not the full story but part of it. Too small filters may be another but I would imagine that would mainly cause vignetting. Is the shutter working fine? Have you inspected its operation?
Greg.
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