Since the introduction of shipping zones. Default shipping method ordering mechanism has been removed.

You can still alter the ordering by navigating to:

Wordpress admin -> WooCommerce -> Settings -> Products -> Shipping methods order


Drag and drop shipping methods the way you like and save.


If the new order does not appear, enable temporarily Shipping debug mode.

WooCommerce -> System Status -> Tools -> Shipping Debug mode


http://jeroensormani.com/shipping-debug-mode/