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Possibly what we need to do here is get details on EXACTLY what you have done.
In particular any calibration frames you have plugged in that they are in the right category .... Ie darks in darks not flats etc.
The more detail you give the easier it will be to sort out... Include version of stacker and the format in which you entered the data, plus camera used etc
It does look as though somehow it's been inverted, check the output mode and that embed changes but don't save are ticked in output file.
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