You haven’t described where you are mapping from your pathology_in message to the schema.clinic message – it sounds like the mapping isn’t working somewhere and the message that is passed to your send port is still the pathology_in message.
I’m also thinking that your problem may be coming from the receive side rather than the send side, let me explain: if the error was on the send side, BizTalk will have already found a schema to associate with the message, so if its found a message in the MgmtDb on the way in (the receive port), it shouldn’t then have problems on the send side! I’m therefore thinking that your error is actually on the receive side….
Either way, if you could advise on how you projects are structured and how they are
deployed in BizTalk Applications; it would also be good to get a copy
of the full error you are receiving from the Event Log.
Cheers, Nick.