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With DSS be carefull as to what you apply to the image, minimal is best, don't let it manage color, just stack don't save any changes it makes, let photoshop or other fix your color problem, you can use whichever method you prefer for stacking be it median, average whatever.
Take you exported Tiff or highest bit image you can import into photoshop.
Duplicate the image, and on the duplicate stretch it to find where least detail exists..... Ie blank sky, no nebula no stars etc.
You can use the eye dropper tool to see where your color balance lies.
Using the original image
Go to Tab
IMAGE ... LEVELS.... Down the bottom right select the middle eye dropper, left click in the blankest bit of sky you found and it should balance the color for you. Just make sure you don't clip the histogram.
Quick,n, dirty but it usually works.
I'm sure others will chip in with ideas for you.
if you do too much with DSS, like go overboard with hot pixel removal and cosmetic fixes, it does all sorts of horrors.
Alternatively, you could let your Nikon program decode the raw files into TIFFS first then stack, worth a try, it's been a long time since I used a dslr, but sometimes it used to have problems with RAW formats.
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