If you set Calculat.type for Freight condition type as Percentage, then system will only consider the PO order quantity. System will not check the SKU quantity.
As I've already said you have to give the freight amount as per SKU quantity, only then system will change the freight amount as per GRN - SKU quantity.
Any how you have to give the freight quantity as per SKU unit In PO condition.
Any how, you have to give the uom here (as shown in above), only then system will calculate the freight amount as per SKU unit.