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mmm i don't think i misread your post, but to clarify
your taking lights and darks exactly the same (just putting the tube cap on so to speak)? they will work, theres no possible reason for it not ot work.
you mention that your taking the flats and bias though EOS utils, do you try and add them to the fit files generated from nebulosity? if so irrispective of you saving your CR2 stack as a Fit file they colour information is different.! just the same as your 16 and 32 bit TIFF files. look the same but are different.!
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