I think the issue is that the variable uc_msg_order_logged_in get set to something like the following:

Thank you for shopping at [store-name]. While logged in, you may continue shopping or click here to view your current order status and order history.

It seems when this variable is set you aren't using a token, and it is just set for the admin user.

I emptied the variable in admin/store/settings/checkout/edit/messages and seems to do the trick as code in the uc_messages hook is fine.

Ben