I was able to solve this with help from support at Smart Slider. They pointed out that the div that wouldn’t go away was using absolute positioning and suggested that I add an id to it so that I could then hide it using CSS. I did this by echoing an id name in header.php in the same line where I echoed the shortcode:
<?php
if (is_front_page() )
echo '<div id="front-page-slider"' . do_shortcode('[smartslider3 slider="3"]' . '</div');
else
{ }
# do nothing ?>
Then I had a new id of ‘front-page-slider’ to work with. I could then call that id in the JS I was using to hide the element:
<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
<script>
$(window).scroll(function() {
var y = $(this).scrollTop();
if(y > 250) {
// $('.n2-ss-slider').slideUp();
$('#front-page-slider').slideUp();
}
if (y < 250) {
// $('.n2-ss-slider').slideDown();
$('#front-page-slider').slideDown();
}
if(y+ $(this).height() == $(document).height()) {
$('#front-page-slider').fadeOut();
}
});
</script>
and my problem was solved.