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We really need to get your flats working Leon. I would suggest you need to use darker flats. When you do your flats, use the EOS utility to check out their histograms. Only use a flat where the histogram is around 1/3 of the way across the tonal range. That is only a rough and ready selection but it should get you out of trouble. And don't mix your flats. If you've only got 3 or 4 that fit that histogram level then use only them, don't add any brighter or darker ones.
From memory you are using the automated IP processing aren't you?
BTW, unless you have take your own dark frames and haven't used ICNR AND you are trying to scale your dark frames for a different light exposure time, you don't need to take bias frames. When you or your camera subtracts a dark frame a bias frame is automatically subtracted because it is included in the dark frame anyway.
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