witholding tax for MRKO

Dear SAP gurus,

In our vendor we input several witholding tax code as the vendor can supply various material and service to our company. During MRKO for consignment settlement for this vendor, the settlement document take all the code and during payment, we find out that we pay it less. Is there any way we can influence during MRKO running so that only some witholding tax code will be selected?

Thanks in advance for all your help.