Starting again with my reply.
I created a completely new master bias and dark frames to calibrate the new flats.
Using the Statistics tool, I was able to check the Median value of different exposures - the camera histogram is not a reliable indicator. By converting raw files with AHD and converting to greyscale (as you would to debayer), the K value approximated RGB values. I was just a matter of refining the camera settings - trial and error.
I came up with these settings - so regardless of the method of obtaining the frames, future attempts should be consistent.
At ISO 800 (the setting I generally use for AP), f/3.2, 1/30th second, EV +1 - approximates 60 - 65% on the camera histogram, and gives an ADU of approx 2200 - a little high, but the next settings down increased the error on the lower side of 2048 - on my camera anyway.
Feedback on this effort would be appreciated. I can't be certain of all aspects of the flat frame, though I have taken a lot of care and effort in reaching this stage.