I’ve run into this problem with PageNavi before. My solution is to hijack the $wp_query variable temporarily and then reassign it after closing the loop. An exmaple:
<?php $paged = (get_query_var('paged')) ? get_query_var('paged') : 1;
$args=array(
'post_type'=>'post',
'cat' => 6,
'posts_per_page' => 5,
'paged'=>$paged
);
$temp = $wp_query;
$wp_query= null;
$wp_query = new WP_Query($args);
/* PageNavi at Top */
if (function_exists('wp_pagenavi')){wp_pagenavi();}
if ( $wp_query->have_posts() ) : while ( $wp_query->have_posts() ) : $wp_query->the_post();
/* DO STUFF IN THE LOOP */
endwhile; endif;
/* PageNavi at Bottom */
if (function_exists('wp_pagenavi')){wp_pagenavi();}
$wp_query = null;
$wp_query = $temp;
wp_reset_query(); ?>
The last step is to reassign the $wp_query variable to what is was originally and then reset the query back to start.
*Edit:*Fixed php tag. Good eye sniper.