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Ok, sorted out the flats problem now too thanks to Brendan's hints above. The FITS files captured by Nebulosity were classed as color, not RAW. The master FITS flat file, because created from CR2 RAW files, was still RAW. This is what was confusing me - didn't realise FITS files can be different.
So the solution was simply to demosaic the flats master and use that. All good now. Thanks Brendan.
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