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Make sure your flats are well into the histogram, so space at either end,
As with all these things consistency is the key, same temperature, gain, etc for everything, don’t mix and match stuff,
CHECK THE FITS HEADER ON YOUR CALIBRATION FILES perhaps gain offset settings are different, some capture programs require you to set them each run (QHY does)
If you’re doing Tshirt Flats they will likely be different as you can’t control the light well, if this is the case it’s seperate dark flats for each filter, don’t mix and match.
Try the Deepsky stacker program, it’s free and I’ve never needed anything else.
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