It looks like the ID and Class for your smoothmenu has DEACTIVATE added to the end of it. When I remove the DEACTIVATE in my browser, it looks almost right. I'm not sure why that's happening, so I would look into smoothmenu (which I know nothing about :( sorry) to find out why it might be adding DEACTIVATE to the ID and Class. Once you figure that out, the "Menu Shadow" will probably start to work again.
Besides the DEACTIVATE causing issues, the WordPress function I use (wp_nav_menu) wraps up the menu in a div by default. When you remove the DEACTIVATE, the menu isn't tall enough, but removing the wrapping div fixes that.
So I will add an option to the Nav Menu Items that allows you to choose if the menu is wrapped in a div or not. My weekend's busy with a bit of WordCamp Milwaukee, but look for an update towards the end of the weekend or Monday.
With all that in mind though, do you plan on making that menu change depending on the page you're on? I ask because that's where this plugin shines. If not, it's probably more appropriate for you to use wp_nav_menu directly, since it gives you more granular control over your menu.