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Ah, looks like the sticky menu is added after the script is executed so these links aren’t included. A solution could be to use a delegated event :

$(document).on('click', 'a[href*="#"]:not([href="#"])', function() {

Instead of :

$('a[href*="#"]:not([href="#"])').click(function() {

If you’d like to keep a bit of space between the header and the point to which is being scrolled, you could just subtract a few pixels :

scrollTop: target.offset().top-$('.isStuck').height()-10