i think the problem is that the flat scaling is wrong when there's no calibration of the flats. since the flats were probably not taken with in-camera noise reduction, you'll probably have to do the calibration of the lights manually. BPP will try to calibrate the flats and lights with any bias frames that you use, and since the lights were taken with ICNR, they are already bias (and dark) subtracted. so BPP will mess everything up.
what is the duration of the flats? if they are short enough you can just make some bias frames, then manually calibrate the flat subs with a master bias made from those bias subs. then you can try calibrating the lights only with the calibrated master flat and see what happens.
so: ImageIntegration on the bias subs (no scaling/weighting), save the integration as master bias, then ImageCalibration on the flat subs with only the master bias, then ImageIntegration of the calibrated flat subs (multiplicative normalization, weights either don't care or average signal strength), then save that integration as the master flat. finally IC on the lights, using only the calibrated master flat (make sure to leave "calibrate" unchecked), and then StarAlignment on the calibrated lights and finally ImageIntegration on the registered lights.
rob
rob