Sorry if I misunderstood your problem
I believe there should not be any problem depending on what the technology that you use and the service provider uses, as long as you both use the same
Soap version. That is the core benefit of using a web service.
The beans generation may be different based on different web service frame works as the vendors would use their own binding mechanism, but JAXB is one standard binding technique that everyone wants to move to.
Still the XML generated out of the beans would be same, irrespective of the binding technique. If you still see some differences I think you can use custom handlers to tamper requests and responses