Thanks for the quick response, @pilou2, it is much appreciated. I'm off to configure my testing site with that information and will hopefully have some idea of where the issue lies later today.

The sub-total calculations for the shopping-cart page's display are performed by the page's header_php.php, first via call to the shopping-cart class' show_total method, with the returned value then formatted into the currently-selected currency.

During the checkout, the subtotal calculation is performed within the order-class' cart method. The overall total and tax are further manipulated by the various order-total modules to produce the order's final tax and total.