Featured Posts Code – Repeated featured posts

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After discussing in chat and seeing the parent index.php file:

http://pastebin.com/27r0FJ3x

The main loop in loop.php is not actually the main loop at all:

<div id="main" class="<?php echo $containerWidth; ?>" role="main">

            <?php get_template_part('breadcrumbs'); ?>

            <?php if ( have_posts() ) { ?>

                    <?php while ( have_posts() ) { ?>
                            <?php the_post(); ?>
                            <?php get_template_part( 'loop', get_post_format() ); ?>
                    <?php } // end while ?>

                    <?php get_template_part('pagination'); ?>

            <?php } else { ?>

So I suggest moving the featured post code into a featured.php, and adjusting index.php as so:

<div id="main" class="<?php echo $containerWidth; ?>" role="main">

            <?php get_template_part('breadcrumbs'); ?>
            <?php get_template_part('featured'); ?>

            <?php if ( have_posts() ) { ?>

                    <?php while ( have_posts() ) { ?>
                            <?php the_post(); ?>
                            <?php get_template_part( 'loop', get_post_format() ); ?>
                    <?php } // end while ?>

                    <?php get_template_part('pagination'); ?>

            <?php } else { ?>

And then adjusting loop.php accordingly