Partial Backorder showing incorrectly on invoice

Here is the scenario:

Customer orders 6 items
We are only able to fulfill 4.

We adjust this in the fulfillment, it prints out on the packing list accurately, sometime it prints out on the invoice correctly (qty this shipment 4). Sometimes it prints out incorrectly: qty this shipment 6

When we fulfill the remaining 2, it prints out correctly on the packing list, but always on the invoice it will show incorrectly: qty this shipment 6 -- although the amount billed reflects the actual number sent.

We used to be able to go in and manually change the invoice so that it would show the correct amount in qty shipped, but are no longer able to do that.