There was an issue with the plug-in that prevented any WP classes from being retained, regardless of the site owner’s preferences.
That issue has been resolved, and is now available in both the WP Repo:
http://wordpress.org/extend/plugins/navigation-menu-ids-classes/
And on GitHub:
https://github.com/aarontgrogg/wp-plugin-navigation-menu-ids-classes
Thanks,
Atg