I tried Your code and with my taxonomy
<?php $questions = new WP_Query(array(
'post_type' => array('studies'),
'post_status' => 'publish',
'posts_per_page' => 15,
'paged' => get_query_var('paged'),
'nopaging' => false,
'tax_query' => array(
array(
'taxonomy' => 'studies',
'terms' => 11
)
),
'orderby' => 'menu_order',
'order' => 'ASC'
));
?>
<div class="grid9">
<div class="entry-content">
<?php if ($questions->have_posts()): ?>
<ul class="list normalize">
<?php while ($questions->have_posts()) : $questions->the_post(); ?>
<li>
<h3><a href="<?php the_permalink(); ?>"><?php echo get_the_title(); ?></a></h3>
</li>
<?php endwhile; ?>
</ul>
<?php endif; ?>
<?php
wp_pagenavi( array( 'query' => $questions ) );
?>
This works fine ,Don't forget to use wp-pagenavi plugin.