This is issue came after updating to WooCommerce 2.0....
I have set up flat rate shipping with some custom options.
The options view in the checkout as radio buttons. When selecting a radio button the total is updated, however when the total is refreshed the radio button is no longer selected.
When pressing 'Place Order' the error "invalid shipping option" appears.
The clients site is now unable to take orders which is unacceptable.
Our theme has been updated to the latest version yesterday.