It's tough to say without looking at all of your code, but I would probably put a URL parameter on the end of your nav links. You mentioned that clicking a link to change your content will also reload your page, right?
Well, on all of the links in your nav, put a parameter like this:
<a href="pageName.php?firstLoad=N">Page Name</a>
Then at the top of all your pages where you include the nav:
<?php
if($_GET["firstLoad"] == "N") {
echo '<nav class="main fadeInRight">';
include('template/nav/main.php');
echo '</nav>';
}
else {
echo '<nav class="main animated fadeInRight">';
include('template/nav/main.php');
echo '</nav>';
}
?>