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Actually, one thing I did not think to ask, were you using any filter? You mentioned having three distinct peaks in the histogram, one for each colour channel (As you would expect) Were all three peaks away from the sides of the histogram with no stretch applied? If any one channel is clipped on either side of the histogram the flats won't work correctly as the data range will be skewed.
I mentioned the filter as when I was using a HA filter or an Oiii filter with my 2600MC I had to skew the requested average ADC for the flats downward to account for in the case of HA, three in four pixels having virtually zero data (Given the signal shows up almost entirely in the red pixels) and for Oiii one in four without much data.
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