Applying discounts to Lines Only

We migrated to R12 on September, 2009. Since then, our Payment Terms that are set up to apply discounts to the Lines Only are not working as they did in 11i.  The discount is being applied to the entire invoice as if the Payment Term had been set up to be applied to the entire invoice amount including the taxes.  We did not change our payment terms when we implemented R12.  Previous to R12, the discounts were applied to the line amounts only. I cannot find any indication that anyone else on R12 is having this issue. This implies that our set up of Oracle contains an error, but I cannot find anything regarding our set