Hi Duncan, I'm not sure why DSS does this, it does to me as well. I use Photoshop afterwards to set the white point accurately, set the black point to not clip the data and then use the gray scale to set the mid tone/ reduce the greying. Try playing with your levels while watching your histogram in Photoshop. If you setup DSS with the recommended settings, it should align the channels and get rid of the blue sky also. Maybe purchase Jerry Lodrigus's book "Photoshop for Astronomy", it is a great resource and can be attributed to the step forward in my images.
Good luck!
