When you check the box “Show (hidden categories)," the hidden ones are always shown checked. The check mark only identifies them as hidden. It doesn't indicate if they are selected or deselected.
I found that you can select/deselect hidden categories by clicking the ones you want to be changed which clears their checkmark. If you say OK or change tabs then return to the Category tab, the unchecked hidden categories, including the one you cleared will again be checked so you can't tell if it's selected. In other words, it toggles them on or off.