re:
<?php get_template_part('pagination'); ?>
what is the full code of the pagination.php file?
what happens if you add instead (per Codex http://codex.wordpress.org/Function_Reference/next_posts_link#Usage_when_querying_the_loop_with_WP_Query ):
<?php next_posts_link('next',$the_query->max_num_pages); previous_posts_link('prev',$the_query->max_num_pages); ?>