How is the withholding tax working on matched to PO invoices?

We have paid the prepayment invoice which has 3 lines. one is not applicable for WHT. The other 2 lines has different WHT rates. On prepayment WHT correctly calculated. But when we have created the Standard invoice and matched it to PO. Applied prepayment to that invoice and after that paid it. As we use withholding tax calculation on payment. When we checked the calculated WHT it seems incorrectly calculated. it should be 6593.93 but instead it is calculated 3767.96. WHt on prepayment invoice was calculated 2825.97. So I think that 2825.97 amount was deducted 2 times. 9419.89- (2825.97 * 2) = 3767.96 but should be 9419.89- 2825.97 = 6593.93. Please advice.