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The black spots may have indicated a temperature difference between the time you took youir lights and the time you took your darks. It may also depend on how your darks are combined and then subtracted from the lights. Do you combine your darks and then subtract from individual lights or do you subtract the dark after the lights have been combined. Also do you use median combine or average?
It's not unusual for galaxy shots to come out looking like a greyscale image. The IR filter in the camera does a pretty good job of filtering out the more subtle low end red colours.
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