issue with menus

Today I went in to rearrange the pages under our custom drop-down menu. After hitting save, the website now showed all kinds of weird menu options.

The only way I can get our custom menu to show is by going over to the tab that says Menu Locations and selecting that menu in the first box for “Header Menu.” But if I go and try to change anything in that custom menu, the custom menu is replaced by the weird menu options, and also several pages from my menu have disappeared. Can anyone help me figure out what is happening?

I am using the graphene theme.