Address copying does not work if there are form errors before you activate the checkbox

Address copying use what's created in Drupal Commerce core now - which is in dev. I don't know if that is what you do use - but moving it there for it to get resolved.

Yeah, from the looks it was originally based around Commerce's address copying but then transformed into a potential Shipping issue. Can you update the issue title when you recheck the problem?

On further testing, I can't confirm this bug. If I do the same process without using your rule to automatically apply shipping to orders on update, it works just fine. I think the problem is with your rule. The way the module works, you're not really supposed to be adding shipping like this, and especially not on an event that's going to be so constantly used as "After an order has been updated." Note that this is going to reapply shipping every single time the order is saved, even if the customer selected a different service or long after the order has completed checkout.

The particular error you're getting doesn't make sense if your order does in fact have the commerce_total price field on it (see the "Field list" report to confirm). If that field is there, then all I can figure is there's something jinky in the combination of rules you're creating, since there's another default rule that manually deletes shipping line items under certain conditions. The fact that this centers around address copying feels like a red herring, but it could be that in my work on address copying with respect to automatic recalculation of shipping services I have changed something that removes this error.

I encountered this issue also. The error occurs inside the validation callback of the checkbox:

function commerce_customer_profile_copy_validate($element, &$form_state, $form)

The issue is that the $form_state['order'] inside this function is already stale. The order inside this $form_state may contain commerce_line_items (shipping) that already has been deleted / "order updated" in the other form hooks in commerce_shipping.checkout_pane.inc.

Here's a temporary patch:

Index: profiles/commerce_kickstart/modules/contrib/commerce/modules/customer/commerce_customer.module
===================================================================
--- profiles/commerce_kickstart/modules/contrib/commerce/modules/customer/commerce_customer.module	(revision 3818)
+++ profiles/commerce_kickstart/modules/contrib/commerce/modules/customer/commerce_customer.module	(working copy)
@@ -1300,6 +1300,7 @@
  * Element validate callback: Pertaining to the "copy profile" checkbox.
  */
 function commerce_customer_profile_copy_validate($element, &$form_state, $form) {
+  $form_state['order'] = commerce_order_load($form_state['order']->order_number);
   $triggering_element = end($form_state['triggering_element']['#array_parents']);
   $pane_id = reset($element['#array_parents']);

A better solution may be having a proper $form_state['rebuild'] = TRUE in one of the checkout panes.