I just recently on a dev site update to WP3.9 and to the latest version of the BuppdBusiness theme as well as updated to BB 2.0. Mostly fine. But for some reason which I can only guess has to do with the admin bar at the top, the menus (one at the top and one at bottom) are moved down by about the height of the admin bar. Strangely, this doesn't happen on the home page.
I know I will have to make you a user so you can see.