When does it happen? Can you show a screenshot including the layers panel as well? Is the padding applied directly on the component?
The only time the checkbox is greyed out for me is on an instance of a component, that has padding enabled. You can only edit the value on instances, but can't disable it. I can, however, disable it when editing the main component.
Sorry to hear you are unable to remove the padding from the component. I am unable to reproduce it at my end on XD 36.1 windows10 machine. I would request you to please try this on a new component and share results with us.