Thank you Giba!
Yes I have now gone back and changed the call from the Business Service to act synchronously and this has rectified the issue! The simplest way to do this was to set the Ack Mode to 'application' so that a new message was not received on the Service until the process had sent back an application Ack for the previous message (which it does at the end of the process).
Many thanks for all of your help solving this!
All of my Business Service CALLS are already set to synchronous (see below), this is why I find this issue confusing?
I have posed the traces of both messages below. The process makes several calls to the operation. As you ca see by the timings in the trace window, Message 2 is in the process making calls during the time that Message 1 is still in the process? Could the BPL be starting to process Message 2 inbetween processing Message 1? (whilst waiting for Call Responses for Message 1?)
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