Pages randomly moving out of main navigation to unlinked

I am having issues with all the pages in my main navigation (the home page and all the linked pages) mysteriously moving on their own, down to the not linked section. I will move them back up into the main navigation, and then I find they have moved back down to the not linked section. This has happened twice to me and I would love to know what's going on and more importantly how to resolve this issue.