I’m far from an expert, but this worked for me….on May 27, 2014
I went into Appearance > Menus. At the top of the menu page, there are two tabs, “Edit Menus” and “Manage Locations.” I clicked on the “Manage Locations” tab. Since I wanted to change my Header Menu, I clicked on the “Header Menu” drop down box, found the menu I wanted. Then I clicked on “Save Changes.” Just to check it, I changed the order of my menu structure and it was changed.
It worked for me. Hopefully, it’ll work for you.