Why can’t we test this quickly and why won’t you let me help you?
Because you don’t need to, i know what the problem is. My point is that the program has a built in indication next to the lights “B”, “F” but that indication has no meaning when you load all masters and lights. Furthermore there is no check done by APP for this so it just starts to stack. There needs to be a diagnostics step that tells the user what is wrong at this point. And there needs to be a short, clear workflow with just the steps for calibration of DSLR images with flats taken at a different iso setting.
A suggestion from me that will save you a lot of headaches in the future is to (And this is as we say in the Netherlands “Cursing in Church”) Add the following checkmark/option: “Calibrate flats with same (ISO/Gain) bias as Lights”