Multiple loops result in double pagination

I’m developing a really complex site that uses a series of category templates to uniquely display the content. Because I require more than one category template, I’ve had to create a new loop for each. To do so I’m using:

<?php $my_query = new WP_Query($query_string . “&cat=1&posts_per_page=15”);
while ($my_query->have_posts()) : $my_query->the_post();
if ( $post->ID == $do_not_duplicate ) continue;
update_post_caches($posts);
$do_not_duplicate = $post->ID; ?>

This works great in allowing me to use unique templates for each category, but for some reason, it is doubling the amount of pages in the pagination.

My index.php has 80 pages of content, but the numbered pagination shows 156 pages. Anything past 80 is empty content.

For the other sections that only have 3 or 6 pages, nearly double the amount of pages is still being added to the pagination. The excess pages being empty as well.

Is there anything in my loop above that would be causing this?