Key to this was the $paged parameter and putting it in the correct query
New code for getting the paged parameter for a ‘page’
if ( get_query_var( 'paged' ) ) { $paged = get_query_var( 'paged' ); }
elseif ( get_query_var( 'page' ) ) { $paged = get_query_var( 'page' ); }
else { $paged = 1; }
The first query (I don’t think I need orderby as I am custom ordering the results by lng/lat)
$args = array();
$args['post_type'] = 'properties';
$args['post_status'] = 'publish';
$args['posts_per_page'] = -1;
$args['orderby'] = 'ID';
$args['order'] = 'ASC';
The second query
$args2 = array(
'post_type' => 'properties',
'post__in' => array_keys($results),
'posts_per_page' => get_option('posts_per_page'),
'offset' => ($paged -1) * 9,
'paged' => $paged,
'orderby' => 'post__in',
'order' => 'ASC',
);
Hope this helps someone in the future