So many things could be going on here, it's hard to say without a link to your site. I can tell you Spun's menu has not been updated recently, so I doubt this is a problem with the theme.
It could be:
* Your data or configuration was changed. Do all your Pages still exist?
* Your menu configuration has changed. "Automatically add new top-level pages" is a WordPress core function. Is the option still checked? Have you tried recreating the menu and reassigning it?
* You're probably running a plugin to display Login/Logout, since that's not a function of the theme, or WordPress itself. Is the plugin not working? You may need to check with the plugin author.
* Another plugin is causing a conflict. Deactivate all plugins and reactivate them one by one to find the culprit.
* You're using custom CSS to change the display of the site, and the menu has been accidentally hidden or changed. Revert any custom CSS.