In the end I created the web service from scratch. There is still some work to do to make it more conformant with standard web services but it's about there.

The solution was essentially take full control of the service and when it came to return the XML I wanted I loaded it into a new DOMDocument() and then returned the XML that way.

Thanks for the help peej.

I guess the solution hasn't been found from the original question's point of view so if anyone has more to add to this thread at a later date that might be useful to all.