com.sun.org.apache.xml.internal.serialize.DOMSerializerImpl.writeToString outputs double "<?xml version="1.0" encoding="UTF-16"?>" since JDK b71.
b70 works ok.

To reproduce problem run the following code

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import java.io.*;
import java.net.*;
import java.security.*;
import javax.xml.parsers.*;
import org.w3c.dom.*;
import org.w3c.dom.ls.*;
import org.w3c.dom.traversal.NodeFilter;
import org.xml.sax.*;


public class filterTests {

    public static void main(String argv[]) {

        DOMImplementationLS implLS = null;
        String xml1 = "<?xml version=\"1.0\"?><ROOT><ELEMENT1><CHILD1/><CHILD1><COC1/></CHILD1></ELEMENT1><ELEMENT2>test1<CHILD2/></ELEMENT2></ROOT>";

        Document doc = null;
        DocumentBuilder db = null;

StringBufferInputStream is = new StringBufferInputStream(xml1);

        try {
            db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
            doc = db.parse(is);
        } catch (Throwable t) {
            t.printStackTrace();
System.out.println("Failed " + t);
        }

        DOMImplementation impl = doc.getImplementation();
        implLS = (DOMImplementationLS) impl.getFeature("LS","3.0");

        LSParser parser = implLS.createLSParser(DOMImplementationLS.MODE_SYNCHRONOUS,"http://www.w3.org/2001/XMLSchema");


        LSInput src = implLS.createLSInput();
        src.setStringData(xml1);

        LSSerializer writer = implLS.createLSSerializer();

System.out.println("");
System.out.println(writer.getClass().getName());

        // set filter
        writer.setFilter(
            new LSSerializerFilter() {
                public short acceptNode(Node enode) {
                    if (enode.getNodeName().startsWith("CHILD"))
                        return FILTER_REJECT;
                    return FILTER_ACCEPT;
                }

                public int getWhatToShow() {
                    return NodeFilter.SHOW_ALL;
                }
            }
        );

        Document doc2 = parser.parse(src);

        String res = writer.writeToString(doc2);

System.out.println("");
System.out.println("res " + res);

        System.out.println("OKAY");
    }
}
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Sample output:
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java version "1.6.0-rc"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.6.0-rc-b71)
Java HotSpot(TM) Client VM (build 1.6.0-rc-b71, mixed mode)


com.sun.org.apache.xml.internal.serialize.DOMSerializerImpl

res <?xml version="1.0" encoding="UTF-16"?>
<?xml version="1.0" encoding="UTF-16"?>
<ROOT><ELEMENT1/><ELEMENT2>test1</ELEMENT2></ROOT>
OKAY
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