Custom post type / taxonomy rewrite archive page 2 gives 404

I've followed the code based off this and everything is working perfectly -How to create a permalink structure with custom taxonomies and custom post types like base-name/parent-tax/child-tax/custom-post-type-name

So I am able to browse taxonomy archives with

my/category
(or)
my/category/subcategory

and view a custom post associated with each term as

my/category/subcategory/custompost

However, I cannot view

my/category/page/2/
or
my/category/subcategory/page/2/

It gives me a 404.

Here is the code I am using.

posttype.my.php

function create_my_posttype() {
    register_post_type(
        'my',
    array(
        'labels' = array(
            'name' = _x( 'Mys', 'post type general name' ),
            'singular_name' = _x( 'My', 'post type singular name' ),
            'add_new' = _x( 'New My', 'add new singular name' ),
            'add_new_item' = __( 'Add New My' ),
            'edit_item' = __( 'Edit My' ),
            'new_item' = __( 'New My' ),
            'view_item' = __( 'View My' ),
            'search_items' = __( 'Search Mys' ),
            'not_found' =  __( 'No Mys Found' ),
            'not_found_in_trash' = __( 'No Mys found in Trash' ),
            'parent_item_colon' = '-:-'
         ),

        'public' = true,
        'publicly_queryable' = true,
        'show_ui' = true,
        'query_var' = true,
        'rewrite' = array(
            'slug' = 'my/%mycategory%',
            'with_front' = true,
            'pages' = true
        ),
        'capability_type' = 'post',
        'hierarchical' = true,
        'show_in_nav_menus' = false,
        'menu_position' = 50,
        'supports' = array(
            'title',
            'editor',
            'comments',
            'shortlink'
        ),
    )
);
}

add_action( 'init', 'create_my_posttype');

taxonomy.my.php

add_action( 'init', 'create_my_taxonomies', 0 );

function create_my_taxonomies() {
    register_taxonomy(
            'mycategory',
            'my',
            array(
                    'labels' = array(
                            'name' = 'Mycategories',
            'singular_name' = 'Mycategory',
            'search_items' = 'Search Mycategories',
            'all_items' = 'All Mycategories',
            'parent_item' = 'Parent Mycategories',
                            'add_new_item' = 'Add New Mycategory',
                            'new_item_name' = "New Mycategory",
            'edit_item' = 'Edit Mycategory',
            'update_item' = 'Update Mycategory',
            'add_new_item' = 'Add New Mycategory',
            'new_item_name' = 'New MyCategory Name',
            'menu_name' = 'Mycategory'
                    ),

        'query_var' = true,
                    'show_ui' = true,
        'has_archive' = true,
                    'show_tagcloud' = false,
                    'hierarchical' = true,
                    'with_front' = true,
                    'rewrite' = array(
                            'slug' = 'my',
                            'with_front' = true,
            'hierarchical' = true,
                    )
            )
    );
}

main.php

include( 'posttype.my.php' );
include( 'taxonomy.my.php' );


add_filter('rewrite_rules_array', 'mmp_rewrite_rules');
function mmp_rewrite_rules($rules) {
$newRules  = array();
$newRules['my/(.+)/(.+)/(.+)/?$'] = 'index.php?my=$matches[3]';
$newRules['my/(.+)/?$']                = 'index.php?mycategory=$matches[1]';

return array_merge($newRules, $rules);
}

function filter_post_type_link($link, $post)
{
if ($post-post_type != 'my')
    return $link;

if ($cats = get_the_terms($post-ID, 'mycategory'))
{
    $link = str_replace('%mycategory%', get_taxonomy_parents(array_pop($cats)-term_id, 'mycategory', false, '/', true), $link); // see custom function defined below
}
return $link;
}
add_filter('post_type_link', 'filter_post_type_link', 10, 2);


function get_taxonomy_parents($id, $taxonomy, $link = false, $separator = '/', $nicename = false, $visited = array()) {
$chain = '';
$parent = get_term($id, $taxonomy);

if (is_wp_error($parent)) {
    return $parent;
}

if ($nicename)
    $name = $parent - slug;
else
    $name = $parent - name;

if ($parent - parent  ($parent - parent != $parent - term_id)  !in_array($parent - parent, $visited)) {
    $visited[] = $parent - parent;
    $chain .= get_taxonomy_parents($parent - parent, $taxonomy, $link, $separator, $nicename, $visited);

}

if ($link) {
    // nothing, can't get this working :(
} else
    $chain .= $name . $separator;
return $chain;
}

class main_app {
    function __construct() {
    } // end class main_app


}

If anyone can help or point me in the right direction that'd be amazing. I don't want to resort to separate URL slugs for taxonomies and custom post types :\ Do I have to modify the rewrite rule to include something involving "paged" ?

Thanks