Compile and run the following:

---%<---
import com.sun.org.apache.xml.internal.serialize.OutputFormat;
import com.sun.org.apache.xml.internal.serialize.XMLSerializer;
import java.io.StringReader;
import javax.xml.parsers.DocumentBuilderFactory;
import org.w3c.dom.Document;
import org.xml.sax.InputSource;
public class TestXercesSerializer {
    public static void main(String[] args) throws Exception {
        DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
        factory.setNamespaceAware(true);
        String xml = "<root xmlns='urn:root'/>";
        Document doc = factory.newDocumentBuilder().parse(new InputSource(new StringReader(xml)));
        OutputFormat fmt = new OutputFormat();
        fmt.setMethod("xml");
        fmt.setIndenting(true);
        XMLSerializer ser = new XMLSerializer();
        ser.setOutputFormat(fmt);
        ser.setNamespaces(true);
        ser.setOutputByteStream(System.out);
        ser.asDOMSerializer().serialize(doc);
    }
}
---%<---

Under JDK 1.5, and most Mustang builds, it is OK:

---%<---
java version "1.5.0_04"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_04-b05)
Java HotSpot(TM) Client VM (build 1.5.0_04-b05, mixed mode, sharing)

<?xml version="1.0" encoding="UTF-8"?>
<root xmlns="urn:root"/>
---%<---
java version "1.6.0-ea"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.6.0-ea-b45)
Java HotSpot(TM) Client VM (build 1.6.0-ea-b45, mixed mode, sharing)

<?xml version="1.0" encoding="UTF-8"?>
<root xmlns="urn:root"/>
---%<---

But in Mustang b46 it is broken:

---%<---
java version "1.6.0-ea"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.6.0-ea-b46)
Java HotSpot(TM) Client VM (build 1.6.0-ea-b46, mixed mode, sharing)

<?xml version="1.0" encoding="UTF-8"?>
<root xmlns="urn:root" xmlns="urn:root"/>
---%<---

Of course com.sun.org.apache.xml.internal.serialize.XMLSerializer is not public and so this is not a violation of the JAXP spec, but there are surely other clients besides NetBeans' org.openide.xml.XMLUtil.write(...), since there have been a number of bugs in JAXP serialization and until now this class has been more reliable. It ought to be either fixed or deleted or renamed, I think.