Thanks for writing in.
Pro header builder doesn’t support one-page navigation yet, it’s only applicable for the standard header, for now. Please add this code to your global custom javascript as a temporary fix.
jQuery( function($){
$(document).on('click', 'ul#menu-main-menu.x-menu a[href^="#"]', function( e ) {
e.stopPropagation();
$('html, body').stop().animate( { scrollTop : $($(this).attr('href')).offset().top - $(this).parent().height() }, 'linear' );
} );
} );
This is only applicable in your current setup and this may not work in the future. And we can’t cover any snippets and custom codes when it fails due to updates and compatibility issue. You may remove it as well when one-page navigation for Pro header becomes available 
Thanks!