I seem to have fixed the pagination issue with the custom loops, not entirely sure how it works, but it does seem to work. I have changed the custom loop to the following;
<?php
$paged = ( get_query_var('paged') ) ? get_query_var('paged') : 1;
$the_query = new WP_Query( array(
'post__not_in' => get_option( 'sticky_posts' ),
'posts_per_page' => 6,
'paged' => $paged
) );
if ( $the_query->have_posts() ) : while ( $the_query->have_posts() ) : $the_query->the_post();
?>
<?php get_template_part( 'content' ); ?>
<?php endwhile; endif; ?>
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