This article should be used to determine the reasons for invoice underpayment.
Please check that you have not received a debit note for the invoice in question. The email address that's setup to receive debits should be checked.
Please also view your remittance to check that the invoice was paid on to ensure there weren't any deductions on the remittance. Steps to check this are detailed below.
If your invoice has been paid for a lower value on the remittance than it was submitted for, please submit a help request, and the Finance Service Centre will investigate.