I don't know Leon. I'll have to have a play with some of my flats to see if I can reproduce the same effect. It may simply be how your monitor is displaying a low contrast 16 bit image on an 8 bit monitor.
Though why it would only do it with your master and not the individual flats I'm not sure. Do you get the same effect if you use FITS instead of TIFS?
I don't know if this makes a difference but do you have adobe RGB checked in the System Options box or sRGB?