Is there an editable/customisable Tax Invoice that can be emailed to customers on product order (amount owed for ordered product) or on product sale completion (could be sent with the product on shipping).  There is an extension in the marketplace but difficult to tell whether it is suitable and also has not been updated and tested for v1.3.3.

Brian, I have had a similar experience with my setup.  The problem was a functional selection in the shipping module.  I am using the Paypal Commerce module for payment gateway and the Auspost Integration module for shipping.  In my case, I selected one of the options, ie. send by letter post, and the shipping estimate and payment function did not work.  Unselecting that option, and the system used parcel post and everything works fine.

I acknowledge that the modules you are using may be different but may help with the faultfinding with your setup.