I\'m using:
I register custom taxonomy (catalog)
Put this into your "functions.php" and then regenerate permalinks. It works to me!
function taxonomy_rewrite_fix($wp_rewrite) {
$r = array();
foreach($wp_rewrite->rules as $k=>$v){
$r[$k] = str_replace('catalog=$matches[1]&paged=','catalog=$matches[1]&page=',$v);
}
$wp_rewrite->rules = $r;
}
add_filter('generate_rewrite_rules', 'taxonomy_rewrite_fix');
The key is to replace "paged" to "page" into the rewrite rule for your custom taxonomy.
This is my first contribution here. Hope I help you.