Up Header Menu

I’m guessing something is interfering with the css that positions the menu. By default it’s inserted at the bottom of the code them css moves it up to that location. Use Firebug or “view source” to see if this is what is happening. The other possibility is that the code that builds that HTML isn’t executing, but I’d think you’d see bigger issues in that case.

The most likely culprit would be a plug-in or child-theme. You could try the classic approach and turn off plug-ins one by one until the problem disappears.

If none of this helps, a link to the site would be more useful than a screen shot.