You actually will have a balance of 100 if you enter 1100 from the paper while the system proposes 1200 , hence you should never be able to post 1200 to the vendor.
An older OSS note 107626 - Selection vendor and delivery costs with a fix for a design error in Release 4.0
explains as solution: If you enter the purchase order vendor as a selection vendor, now the system only selects the delivery costs for which this vendor is entered as a conditions vendor.
so it seems that your system does either act differently (then open an incident at SAP) or you do not have a vendor in the conditions.