First let me begin with saying that this is a great plugin and fits my needs exactly!
Well, almost exactly. I am using this theme http://www.elegantthemes.com/preview/LeanBiz/ for my site (http://swami.wustl.edu/wordpress/). In the theme options, you can specify which pages are not shown in the navigation bar. For example, I've chosen not to show the page "Publications" because I'd like it to appear within the slider instead.
I've also set the user level for the Publications page so that everyone can view it. As you can see, this setting seems to be over-riding the theme setting and seems to be forcing the page Publications to appear in the navigation bar.
This same over-ride occurs for blog categories as well. Do you think you could fix this? Thank for your help!