OK, now I see what you're talking about. Thanks for changing the uploads.
I can't tell from your description if you are double subtracting the bias signal from your lights and/or flats. Please consider doing to following to check whether or not that's what's going on here.
I recommend that you do the following as a test:
(1) Make a master dark by combining (using ImageIntegration) your uncalibrated darks. Hopefully your darks are of the same temperature, exposure, etc. as your lights as this step may not work well. If they are not matched well, this is something that you can easily correct by taking some more dark frames to match the lights.
(2) Make a master flat by first subtracting just the master bias from each flat frame (using ImageCalibration). Make sure you uncheck any calibration or optimization boxes. Then make the master flat (using ImageIntegration).
(3) Now use ImageCalibration, again with all those calibration and optimization boxes unchecked, to calibrate the lights. Here you include just the master dark and master flat, no bias. Combine these calibrated lights (using ImageIntegration) and see if that does a better job.
Since the bias signal and matching dark current are both included in the master dark that I've described, then you know that you are subtracting both of those just one time from the lights. And you are just subtracting the bias signal from the flats, and here we are assuming for now that any dark signal in the flats is negligible. Following these steps will check to see if your original process was double subtracting something or otherwise not doing what you thought it was. It you are still unsatisfied, there is more to check, and others will likely chime in with more questions and suggestions.
Good luck, and please post your results of this. Feel free to ask any questions if you don't understand my recommendations.