IMO, once you get a calibration you're happy with, stop messing with it. Just go to fill up> OK. Don't change the value. You'll drive yourself mad otherwise.
Overfilling will cause the issue you describe. If you know the original calibration (in percent), you can go into fill up and change it back. Your next fill will be off by the amount you've already used.
If you find a new technique or mod changes calibration over a couple of tanks, then you may wish to recalibrate.
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