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how did you take the flats?
In the past I have taken my flats at twilight. Aim the scope/lens away from the rising or setting sun, towards a neutral part of the sky. then fire away a bunch of shots on apeture priority. Might need to experiment with the exposure compensation so that the flats are not too exposed. (eg you might need to try -1/3 to -1). check the histogram of the flats so that its sitting about midway.
If you take bias/offset shots as well - ie fastest shutter speed you can with the lens cap ON (so like a dark), on the same ISO as the lights, darks and flats - then DSS will automatically scale the darks and use them to subtract from the flats, so that the flats are dark calibrated so they dont add further to the noise of the image. I usually try to work with about 50ish flats and bias frames, and 20-50 darks.
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