My header is:
%logo %image %bar2 %bar2 %bar2 %pages %bar2 %bar2
The disappearance was not, as far as I can tell, related to an update. It was working Monday and there have been no updates since then.
1) I have turned off caching plugin and reverted to clean .htaccess
2) Menu re-appears when I switch to default WP 2105 theme or default 2014 theme (Assuming i tell it to use my custom menu) See screencap at http://imgur.com/BxBoCAp
3) If I switch off all plugins it still does not reappear.
4) Have moved something off the menu and saved the new version of the menu. No luck.
5) Have tried assigning the custom menu to the categories spot and changing my header to reflect the new placement. No luck.
6) Have tried constructing a whole new custom menu and putting it in the categories spot in the header. No luck.