receiving transaction processor mode

We have an interface to a third party WMS system  and we read flat files from them to and read them into our Materials interface and receiving interface tables.   When we create an inter-org requisition in one org to ship product to another org we seem to have an issue.   The shipping part seems to flow fine, but the receiving part causes issues.  We send an expected receipt (Oracles Shipment Number) to the WMS receiving site.  When that site completes the receipt is send a receipt completion to Oracle in the form of a flat file with one receipt line