Same issue here. I had a “top” menu and a “footer” menu. Could not get the “top” menu to show at the top, it always showed the “footer menu.” After reading this post, I deleted the “footer” menu and, sure enough, the top menu showed up where it’s supposed to. Of course, now I have no footer menu. Hmmm.
I went back and fiddled some more and found that I could get the “top” menu to show in the footer area, but the “footer” menu always shows in the top area. I inspected the CSS – just looking for a clue – and found “UL#menu-footer.menu” in my top menu, even when I have it set to use “top”