Voucher discount adjustments

PSFT calculates discounts by excluding freight, miscellaneous charges and sales tax from the voucher amount.  We have a vendor who actually includes freight as part of the discount calculation.  What is the best practice for dealing with the difference in the discount between the PSFT calculation and how the vendor is calculating it?  Right now my user is adjusting the freight amount in order to compensate for the difference in the discount.  We would like to correctly identify the discounted amount and this is not the way to do that.  How are others handling this?