How can I implement jQuery plugin correctly with my CPT?

It looks like you’re looping 4 <ul class="flex-unslider-ul"> items, do you not need to simply put the loop around the <li class="flex-unslider-slide">

<?php
$args = array(
    'post_type' => 'referanse'
);
$referanser = new WP_Query( $args );
if( $referanser->have_posts() ):
    ?>
    <ul class="flex-unslider-ul">
        <?php  while( $referanser->have_posts() ): $referanser->the_post(); ?>
        <li class="flex-unslider-slide">
            <div class="content">
                <?php the_content(); ?>
            </div>
            <h1>- <?php the_title() ?></h1>
        </li>
        <?php endwhile; ?>
    </ul>
<?php
else:
    echo 'Oh ohm no referanser!';
endif;
?>

Hope this helps