Hi Hareesh,
thanks for the tip. I already tried that because ist sounded helpful. However in our current situation the messages (different payload but same JMS message ID) originate from the same MQ Queue and use the same PI communication channel. There's also now way to distinct any messages because they're virtually the same message type. The duplicate JMS ID could happen with any of those messages.
However, I'm not completely sure how the parameter "Set PI Message ID" in the sender CC works. It's currently set to GUID. Does this parameter refer to what is used as PI message ID or does it have something to do with the key that is used when story the actual JMS Messages to the database table "XI_AF_SVC_ID_MAP"?