Wordpress - Pagination not working with custom loop

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.

I had a similar issue earlier today...

Do you have a custom post type and a page or post with the same slug? Meaning is the url of a page you have /real-estate and the custom post type url rewrite at /real-estate ?

If that's the case you can't have 2 with the same url or else wordpress gets confused.

You either can change the url or try this http://wordpress.org/support/topic/pagination-with-custom-post-type-listing?replies=23#post-1637753. I chose to change my url, but someone on there wrote a custom query to get around the problem

I am Using This For Custom Pagination and its work fine

//paginations for newsletter

     //define in function file
      function custom_pagination($numpages = '', $pagerange = '', $paged='')  {

      if (empty($pagerange)) {
        $pagerange = 2;
      }

      /**
       * This first part of our function is a fallback
       * for custom pagination inside a regular loop that
       * uses the global $paged and global $wp_query variables.
       * 
       * It's good because we can now override default pagination
       * in our theme, and use this function in default queries
       * and custom queries.
       */

      if ($paged == '') {
          global $paged;
          if (empty($paged)) {
            $paged = 1;
          }
      }
      if ($numpages == '') {
        global $wp_query;
        $numpages = $wp_query->max_num_pages;
        if(!$numpages) {
            $numpages = 1;
        }
      }

      /** 
       * We construct the pagination arguments to enter into our paginate_links
       * function. 
       */

      $pagination_args = array(
        'base'            => get_pagenum_link(1) . '%_%',
        'format'          => 'page/%#%',
        'total'           => $numpages,
        'current'         => $paged,
        'show_all'        => false,
        'end_size'        => 1,
        'mid_size'        => $pagerange,
        'prev_next'       => true,
        'prev_text'       => __('◄'),
        'next_text'       => __('►'),
        'type'            => 'plain',
        'add_args'        => true,
        'add_fragment'    => '',
        'after_page_number' => '',
        'before_page_number' =>'',
        );
     $paginate_links = paginate_links($pagination_args);

      if ( $paginate_links ) {
        echo "<nav class='custom-pagination'>";
          //echo "<span class='page-numbers page-num'>Page " . $paged . " of " . $numpages . "</span> ";
          echo $paginate_links;
        echo "</nav>";
      }
    }
    ?>

// Define this for any Template like template-newsletter

    <?php  $paged = ( get_query_var('paged') ) ? get_query_var('paged') : 1;
                               $newslatter_detail = array(
                               'post_type' => 'newsletter',
                               'post_status' => 'publish',
                               'posts_per_page' =>4,
                               'order' => 'ASC',
                               //'orderby' =>'date',
                               'paged' => $paged
                               );
                               $posts = new WP_Query( $newslatter_detail );
                               $posts_array = get_posts( $newslatter_detail );
                              if ( $posts -> have_posts() ) {
                               while ( $posts->have_posts() ) : $posts->the_post();
                               the_title();
                               endwhile;
                        wp_reset_postdata();
              } else { ?>
                 No Forum List found.
                <?php } ?>

              <div class="pagination">
                    <?php
                       if (function_exists(custom_pagination)) {
                        custom_pagination($posts->max_num_pages,"",$paged);
                       }
                       ?>
                 </div>