subinventory transfers when using API

We seem to be having an issue with our subinventory transfers when using the pick confirm API

Our system is set up to use consignment goods whereas the goods flow from consignment to staging creating a consumption invoice

I have found that the api is somehow moving the consignment goods first the finished goods which causes a change in ownership but is not producing our consumption invoice

sounds as though it might be a setup issue more than an API issue but my setup for the pick rule indicates to pick from consigment and ship from staging--is the api causing this? can I force the pick confirm to use the proper subinventory transfers?