Symptoms
Account has been created with wrong tax zone. Order was placed for this account, but was not yet processed. The provider changes the tax zone, pushes order for provisioning. As a result, there is invoice and payment for the total different from the order total. The same situation is possible if the tax is changed after order placement.
Cause
The issue is caused by the bug with id #PBA-28752 ("if Calculation Type of tax is changed before invoice generation then invoice will be generated incorrectly").
Resolution
Close the order by applying a credit memo for the tax sum (this will make order to go to CP status) and then, apply a debit memo to this credit memo (to close and nullify the customer's balance).