Looking into this offline, we where able to resolve the problems.
The problem was in the way the checkout page was being created. the Shipping server behavior was being added to the checkout page when it should have been added to the confirm page.
We reran the wizard to have the pages created properly with the shipping server behavior added to the confirm page. This fixed problems 1 and 2.
As for the Third point, "There doesn't seem to be anywhere in any of the pages generated by ecart for customers to provide payment information":
There are no Credit card input fields because Protx only offers Remote Checkout, where the user is transferred to the Payment gateways account to process the transaction.
The user will not enter the credit card information until they get to the Protx site.