Major issues with Reward Points not showing correctly on checkout or invoices

I am working with an OpenCart 1.5.6.4 site for a client, and they are getting issues with reward points. It seems that they are displaying correctly on the Cart, and deducting the right amount - but when the user reaches the checkout, although the reward points show, the total is incorrect as it's not deducting them. And, although the customer gets charged the right amount (i.e. the discounted amount), the invoices in the admin area still show the full price, not the deducted total.

I am trying desperately to find in the code where the order totals are added to the database, with no luck. I am not familiar with the structure of the code, and I'm not even sure if finding it will provide a solution. I've played around with the Order Total sort orders though it makes no difference to the calculation, only the position of the text on the checkout.

Any help with this would be most appreciated, as I am finding it very difficult to solve.

Thank you