Custom Menus Disappearing from Frontend

We are using WordPress as a CMS on a closed network. We intend to have many publishers, some of which will need to rearrange the primary navigation in the custom menus if they fail to choose a parent when creating a page.

However, for the third time in the past fortnight, I have just saved a change to the menu and it has again disappeared from the frontend. I can still see it in the backend, it looks as if there is nothing wrong with it. But it will not show in any method when you view the site.

We have our go-live in two weeks, and we need to resolve this as it’s not something we can afford to happen in production.

PLEASE HELP. I have spent hours trying to solve this, with no joy at all.