Kylie, I’m having the same problem with the same theme. Were you ever able to get the problem resolved? If so, how? I will update here if I find a fix. Thanks.
I did! What I had to do was change the name of the main menu to 1main menu. Because it wants to display them in alphabetical order for some reason.
Kylie, I ran across this thread that indicates a WordPress 4.0 “bug” as far as I can under stand. I’m not a super coder. The only fix I found was deleting all my other menus, including the footer, so the only option so show is the header nav. This is by no means a “fix,” but my header nav menu is much more important on my site than the footer.
https://ww.wp.xz.cn/support/topic/wp-40-broke-main-menu?replies=33
Opps! I just saw you posted! (Should have refreshed my page) That’s a great, and much better fix than my idea! Thanks for following up.