The problem with the menu is directly related to the error thrown by the shortcodes plugin. Since the scripts are printed in the footer and the fatal error prevents the footer from printing, the script that makes the nav menu respond is not loading.
The error is most probably triggered by the shortcodes plugin. Make sure you’re using the latest version. If the error still happens try a different plugin like Easy Bootsrtap Shortcodes, DW Bootstrap Shortcodes or Twitter Bootstrap Shortcodes Ultimate Add-on.