Hi Allen,
Is it possible that you have registered sub options pages, if so, what code are you using?
Have you inspected the DOM to make sure the menu item is not being hidden by CSS.
Have you used a filter on the wp menu to remove any items?
Are you able to change theme, and install ACF / optiosn page like normal plugins? Then, include the options page as a theme include, then ACF, then swap to your theme.
At what point does the issue happen?
