I have found my own answer thanks to the awsome work of [url=http://msdn.microsoft.com/msdnmag/find/?type=Au&phrase=Aaron%20Skonnard&words=exact]Aaron Skonnard[/url]
Aaron has produced [url=http://msdn.microsoft.com/msdnmag/issues/05/11/ServiceStation]An XML Guru’s Guide to BizTalk Part 1[/url] and [url=http://msdn.microsoft.com/msdnmag/issues/05/12/ServiceStation]An XML Guru’s Guide to BizTalk Part 2[/url]
Anyway, the answer is the pipeline completes its processing and then applies the map. Once the map has been applied, it is sent to the MessageBox awaiting subscribers to the mapped message.
Hope this is clear, if not be sure you read Aaron’s work (read it anyway, it’s worth it!)