Posts not ordering on Term Archive pages

Solved the issue. So here is the problem. I had a custom pre-get_posts filter. Sadly, when you apply this, apparently it changes the order back to default unless you specify otherwise. So initially I had:

if ($query->is_search) {
			$query->set('post_type', array('project'));
			$query->set('meta_key', 'list_only');
			$query->set('meta_value', '1');

I had to change that to

if ($query->is_search) {
			$query->set('post_type', array('project'));
			$query->set('meta_key', 'list_only');
			$query->set('meta_value', '1');
			$query->set('orderby', 'menu_order');
			$query->set('order', 'ASC');