I attempted my first-ever set of flats this morning, following the advice of Trevor from AstroBackyard and using the morning sky to light my double layer of tee-shirt stretched over my 8" Newt. I was surprised (although I'm not sure why, in hindsight) that my flats all came out pale blue. I guess the sensor was "seeing" the blue sky through the tee-shirt.
Is this okay? Disastrous? Does stacking software consider the color content of the flats or only the monochrome value?