Losing "xmlns" when transforming DOM to XML file in OC4J

I am outputting a DOM to a file using the standard transformation approach. When executed within JDeveloper everything works fine. However, when wrapped in a webservice using JDeveloper and run within OC4J the output is missing the "xmlns" attribute from the root node. Anyone have an idea why this is happening and what a workaround would be?
The original XML root element is:
<e2579ReportAssemblyList xmlns="http://cdrh.fda.gov/schema/e2579ReportAssembly.xsd" xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" xs:noNamespaceSchemaLocation="http://cdrh.fda.gov/schema/e2579ReportAssembly.xsd e2579ReportAssembly.xsd">
You can see the xmlns attribute has been provide. I have verified that the attributes are correct while in the DOM.
The xml root element after saving to DOM using transformation is:
<e2579ReportAssemblyList xmlns="" xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" xs:noNamespaceSchemaLocation="http://cdrh.fda.gov/schema/e2579ReportAssembly.xsd e2579ReportAssembly.xsd">
You can see the xmlns attribute is now blank.
The approach used in the transformation is as follows:
File mOutput = new File(mFileNamePath);
FileOutputStream mOutputStream = new FileOutputStream(mOutput);
Transformer mTransformer = TransformerFactory.newInstance().newTransformer();
mTransformer.transform(new DOMSource(mNextBatchItem), new StreamResult(mOutputStream));
mOutputStream.close();
Any suggestions would be greatly appreciated.

If no one knows why this is happening in the transform, is there another reliable way of outputting the DOM to an XML file?

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