I’ve disabled all the plugins except pikList and I’m still having the problem. Also I noticed that I did have custom-fields enabled as part of defining the post type

'report' => array(
       'labels' => piklist('post_type_labels', 'Report')
      ,'title' => __('Enter a new Report Title')
      , 'supports' => array( 
      	'title'
      	, 'editor'
      	, 'post-formats'
      	, 'thumbnail'
      	, 'custom-fields' 
      	, 'excerpt' 
      	, 'author'
      	, 'revisions'
      	)

So I took that out. I also put this code in functions:
function fix_metabox() {

    remove_post_type_support( 'report', 'custom-fields', 100 );
}
 add_action( 'init' , 'fix_metabox' );

I did that because of this post:

Meta box does not update when post is Published

I’m using pikList 0.9.9.9

Now 50% of the time the reordering will get saved – the rest of the time it orders by input date ( I think). Anyway – its acting a bit flakey.

Oh -this may be due to an update of WPML.