A user is unable to see application in the Navigation Pane, despite having full access to the table that it points to.
This issue can be caused by having an active override in place.
For example, if there are two applications, "apple" and "orange," and an override is set up to override the apple application with the orange application, the end user will never be able to see the apple application.
To correct this, navigate to 'sys_app_application.list' in the nav pane and filter where 'overrides' is (the application being overridden). Once you have found this, simply clear out the overrides column and save. Add the 'overrides' column to the list if it's not already there.