VAT on new vheicle


We have recently purchased a new vehicle.  Paid the VAT element from business took remaining on finance.  We have entered the purchase invoice in total including the VAT, paid the invoice in two stages, one from our bank account for the VAT the other from the finance company.  Why is the payment from our bank the VAT element not showing on the VAT return.  Checked dates, allocated payment to invoice, we are cash accounting