Typically this is a result of the User Login Part added to the page. Any page which has a User Login part on it will not be displayed within the menu, as the user is already logged in and does not need to log in again. 

To confirm if a User Login part is added to the page and remove it if needed:
  1. While logged in, navigate to the page which is disappearing 
  2. Click Edit this page
  3. Review the page to see if a User Login part is present, if so and you need to cut it, proceed to the next step
  4. Click the gear next to the part
  5. Click Cut