The site url is http://www.theonlinenewbie.com/
I just upgraded to WordPress 3.8.1 and Atahualpa 3.7.13
My header, menu and footer disappeared in the update. I found items in this forum to fix the header and footer, but nothing about the menu disappearing. (There were some very old items about menus, but they didn't seem to apply.)
I have a custom menu and it is set to menu 1 - I tried re-saving that, no luck. Tried saving the menu item in Atahualpa options, no luck.
I don't have a caching program.

Thanks.

if you are using a WP custom menu, go to dashboard->appearances->menu and save the location again.
if not, what do you have in ATO->Style & edit HEADER AREA->Configure Header Area

As I stated in my original post, I am using a custom WP menu, which I have re-saved. In fact, I've re-saved it several times, and the menu still doesn't show up.

The only thing in ATO->Style & edit HEADER AREA->Configure Header Area is:
%image

Thanks.

The only thing in ATO->Style & edit HEADER AREA->Configure Header Area is:
%image

if that is all you have, then that is all you will get. If you want a custom menu or even a Atahualpa aotomatic menu, you have to include %pages or %cats in the 'Configure Header Area' option. the %pages versions will use the menu you assign to 'Menu 1' location (in dashboard->appearances->menu) and %cat will display the menu you assign to 'Menu 2' location (this applis if you use the %page-center also)

This has been in effect since WordPress added Custom Menus.

That worked. Thanks. Not sure why it was okay in the last version and not in this, but as long as it's all there, now, I'm happy.