I suspect you have similary structured menu as I do: one menu container (not a menu in itself) with several sets of lists/buttons (actual menus). So plugin calls two (or more) different menus.
Easiest way is to disable one set of buttons (maybe category buttons) if your theme allows it.
Much more complicated way is to build new different menu and have the plugin call this one. It is unfortunately beyond my grasp to help you with this.
I’ve also tried WP Select Box Navi, which is harder to install and does the same thing. Only goes to show this probleme is theme specific.
Cool solution would be if plugin had the option to rename multiple menus, this would justify two select menus to some degree.
Sorry of not being of any more help.
