The animation is lost probably because of how it is attached to the buttons.
Try changing in theme.js this:
$("a[href=#top]").on("click", function(e) {
e.preventDefault();
$("html,body").animate({scrollTop: 0}, 1200);
});
// Smooth scroll to bottom.
$("a[href=#bot]").on("click", function(e) {
e.preventDefault();
to this:
$(document).on('click', "a[href=#top]", function(e) {
e.preventDefault();
$("html,body").animate({scrollTop: 0}, 1200);
});
// Smooth scroll to bottom.
$(document).on('click', "a[href=#bot]", function(e) {
e.preventDefault();