Menus are sorted based on their weight. When you create a menu you'll see a drop down box where you can select a weight - lighter items "float up" and heavier items "sink down".
For example, if you have a menu item named "Apples" with a weight of 3 and another menu item named "Oranges" with a weight of 2, "Oranges" will appear first or near the top because it's weight is lighter.
If your menus are out of order just edit each one and make a note of its weight - this will help you to find the offending menu item with the incorrect weight assigned to it. Just make sure that you edit your menu items to have the right sequence of weights and your problem will be solved.