Order is not changed in category loop

Out of the box its only changing the main query.

changing a custom query requires custom coding.

ex:

add_action('pre_get_posts','custom_pre_get_posts');
function custom_pre_get_posts($q){
   	if ($q->is_category('board-of-directors')){
   		$t = get_term_by( 'slug', 'board-of-directors', 'category');
   		if ($t){
			$order  = $GLOBALS['in_cat_order']->get_all_category_posts($t->term_id);
			if (count($order)> 0 ){
				$q->set('post__in',$order);
				$q->set('orderby','post__in');
			}
		}
	}
}

I added that code and got the error,

Fatal error: Unknown: Cannot use output buffering in output buffering display handlers in Unknown on line 0

I was able to trace it to your plugin.php file

function get_all_category_posts($cat_id = null){
			if ($cat_id == null) return array();
			$cat_meta = get_option( "in_category");
    		$order = isset($cat_meta[$cat_id])? $cat_meta[$cat_id]: array();
    		$posts = get_posts(array(
    			'post_type' => 'post',
    			'posts_per_page' => -1,
    			'post__not_in' => $order,
    			'fields' => 'ids',
    			'cat' => $cat_id
    			)
    		);
    		foreach ((array)$posts as $p) {
    			$order[] = $p;
    	}
    	return $order;
}

after removing ‘cat’ => $cat_id the error went away.

Of course that creates problems elsewhere so for a quick fix I made a copy of that function without the problematic array entry for the custom_pre_get_post() to use.