Hi,
Are you able to debug the logic (following the BAPI_ISUPARTNER_CREATEFROMDATA call) on ECC side? If not, and if the AND WAIT does not solve the issue (or does not always solve it), could it be that there is some loose coupled logic handler activated for BUS1006.CREATED Event (or some custom Event handler triggered upon creating Business Partner), that needs to lock the Business Partner itself or performs something that in turn locks it..?
You can check the Event type Linkages for BOR Objects in Transaction SWETYPV:
Or switch on Event Trace in SWELS (for the user that perfoms BAPI), and display the trace in SWEL. If that doesen't bring an idea what's going on, I'd go for tracing WF-BATCH in ST12...
cheers,
Janis