Wordpress pagination url 404 error with WP-PAGINATE - wordpress

Question

Would anyone happen to know why the WP-PAGINATE plugin for Wordpress Multisite is repeating one site's home url in the links for page numbers and previous/next arrows? The page is a default posts page which uses no custom posts. All pagination links with the plugin are generating a 404. I've tried updating the permalinks.
Here is an example of the URL that it's giving:
http://www.site.com/a_site_name/a_site_name/page/2
It should be:
http://www.site.com/a_site_name/page/2
Thanks.

Answer 1

I know this post is slightly old...but oh well if it helps someone it helps. I tried using the WP Paginate plugin and it didn't do jack diddly for me so I went with this alternative which solved everything for me.
HTML/PHP:
<?php
//Fix homepage pagination
if ( get_query_var('paged') ) { $paged = get_query_var('paged'); } else if ( get_query_var('page') ) {$paged = get_query_var('page'); } else {$paged = 1; }
$temp = $wp_query; // re-sets query
$wp_query = null; // re-sets query
$args = array( 'post_type' => array('assignment', 'student-post'), 'orderby' => 'date', 'order' => 'DESC','posts_per_page' => 15, 'paged' => $paged);
$wp_query = new WP_Query();
$wp_query->query( $args );
while ($wp_query->have_posts()) : $wp_query->the_post();
?>
This allows several things. One it checks if your on home, page, or single and tells the $paged variable how to react in turn. It also allows you to query your pagination with custom post types. Also by not using query_post you get to avoid some really funky stuff that you sometimes get when using it.
Inside your functions.php
function paginate() {
global $wp_query, $wp_rewrite;
$wp_query->query_vars['paged'] > 1 ? $current = $wp_query->query_vars['paged'] : $current = 1;
$pagination = array(
'base' => #add_query_arg('page','%#%'),
'format' => '',
'total' => $wp_query->max_num_pages,
'current' => $current,
'show_all' => true,
'type' => 'list',
'next_text' => '»',
'prev_text' => '«'
);
if( $wp_rewrite->using_permalinks() )
if ( is_home() ) {
//fixes index.php weird error on how it displays the pagination URL which causes errors only on index.php
$pagination['base'] = user_trailingslashit( trailingslashit( remove_query_arg( 's', get_pagenum_link( 1 ) ) ) . '?page=%#%/', 'paged' );
} else {
$pagination['base'] = user_trailingslashit( trailingslashit( remove_query_arg( 's', get_pagenum_link( 1 ) ) ) . 'page/%#%/', 'paged' );
}
if( !empty($wp_query->query_vars['s']) )
$pagination['add_args'] = array( 's' => get_query_var( 's' ) );
echo paginate_links( $pagination );
}
This originally came from http://bavotasan.com/2011/simple-pagination-for-wordpress/ with me slightly modding it to get the pagination to work on the homepage.
This, again, does several things. It paginates your page with each page getting it's own link (which I find nice) and it also re-writes the URL to allow for pretty permalinks. The For some reason wordpress gives a 404 page on the index.php so I changed 'page/%#%/', 'paged' ); to '?page=%#%/', 'paged' ); and wrapped it in a conditional for is_home(). This fixed my issues with pagination and pretty permalinks.
Optional Styling of Pagination
ul.page-numbers {
margin: 20px 0 10px;
width: 100%;
padding: 0;
font-size: 12px;
line-height: normal;
clear: both;
float: left;
}
ul.page-numbers li {
float: left;
}
ul.page-numbers a,
ul.page-numbers span {
border-radius: 3px;
-moz-border-radius: 3px;
-webkit-border-radius: 3px;
background: -webkit-gradient(linear, left top, left bottom, from(#E4E3E3), to(#FFFFFF));
background: -moz-linear-gradient(top, #E4E3E3, #FFFFFF);
filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#E4E3E3', endColorstr='#FFFFFF');
padding: 3px 4px 2px 4px;
margin: 2px;
text-decoration: none;
border: 1px solid #ccc;
color: #666;
}
ul.page-numbers a:hover,
ul.page-numbers span.current {
border: 1px solid #666;
color: #444;
}

Answer 2

To fix this, what I did is open up wp-includes/link-template.php and comment out line 1389 replacing it with the following:
//$home_root = preg_quote( trailingslashit( $home_root ), '|' );
$home_root = preg_quote( $home_root, '|' );
(Wordpress version used is 3.3.1)