JDOM to DOM conversion generates DOM Documents which are not namespace aware ; no way to work around this in JDOM.
At time 1.0.3 was released, a quick and dirty patch has been added to bc-soap to prevent generation of these double namespaces (bc-soap, commit r15184).
Remember to recheck this test case newt time Prosodie test cases will be run, to reproduce the problem and fix it properly by removing jdom DOMOutputter in se-bpel, and replacing it with an XMLOutputter, which should fix properly the problem.
Remove related hack in bc-soap.