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Tony, RAW is just that, no noise reduction, colour balance correction or sharpening applied. I am fairly sure that setting long exposure noise reduction has no effect on the RAW file. I made the same mistake with McNaught, took images in RAW without manually taking darks or flats, they were really noisy as well but the duplicate JPG's taken with long exposure noise reduction set were fine as the camera automatically subtracts a dark frame.
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