I open a page to Edit. Tick any one or all of the Disable Elements options ( Header Navigation Headline Footer ) and click Update.
When Edit page refreshes, the tick boxes are all unchecked, and the page is unchanged.
I have disabled all other plugins except yours.
Can you try adding a new page and then trying the options?
I’ve seen it where someone has been using a page template with a different theme, then they switch to the new theme and the page template doesn’t exist anymore. Then WordPress ignores any saved changes inside metaboxes for some reason.
If the options work with a newly created page, then that’s the issue.