We have developed an application that uses the DOMBuilder class to generate a JDOM document from a DOM document.
You need to make sure that you don't have some old version of XML jar files in your classpath or in ext dir. Replace such files by xerces.jar file and you should not get this error. Note that the jar files which are dropped into ext dir are searched before the jar files in classpath.
Also please refer to similar problem while installing cocoon in tomcat setup.