@brendon: In next version, we will remove the header of the Menu. So, you don’t need to add any of these script. You can just remove it after next version update. Yes, I understand there is delay in the script. Can you try moving it to “Appearance => Theme Options => Tools => Header and Footer Codes => Code to display on Header” box as below:
<script type="text/javascript">
jQuery(window).load(function() {
//Remove Old Primary Menu
jQuery( "#tinynav1" ).remove();
//Remove Old Footer Menu
jQuery( ".sb-holder" ).remove();
// Secondary Menu
jQuery('#access-secondary .menu').tinyNav({
active: 'current-menu-item',
header: ''
});
jQuery(".tinynav2").selectbox();
});
</script>