I am having a similar problem. I can not get my site to work with postname ever since installing 3.7.1. I am not sure what is going on and have searched the world over. I am getting the server 404 and not the wordpress handler 404.
I have tried everything except a total re-install which I hope not to have to do.
It seems that by commenting out the wp_nav_menu_object you get the desired result of only working in the main menu. At this point I do not understand the code well enough to comment further.
//add_filter( ‘wp_nav_menu_objects’, array( &$this, ‘wp_nav_menu_objects’ ) );
