If you look you will probably see that the <div id="custom_menu" ><ul> tag is taking up all the space left in the header, so try setting a width for the custommenu something like...
#custom_menu ul { float: left; width: 75%;}
That should allow the message and user menus, which are floated to the right, space to land after the custommenu. At the moment they are being pushed down.