XML message parsing using XSD - xsd

Question

An xml message is received through a JMS listener and the message is validated against an XSD. Though the message is valid, at times the message is considered to be invalid and the following exception is raised.
The xml message in not encoded with UTF-8, the message just starts and ends with root.
Msg Format :
<root>
<Message>Sample Message</Message>
</root>
What could be the issue that is causing the message to be invalidated though it is valid.
Websphere server - 6.1
JDK version 1.6
Spring version - 2.3x
Parser Code :
InputStream inputStream = getResource().getInputStream();
Source schemaSource = new SAXSource(new InputSource(inputStream));
Schema schema = getSchemaFactory().newSchema(schemaSource);
ValidatorHandler validatorHandler = schema.newValidatorHandler();
validatorHandler.setContentHandler(this);
parser = getParser();
parser.setContentHandler(validatorHandler);
InputStream iStream = new ByteArrayInputStream(asyncMsg.getBytes());
InputSource inputSource = new InputSource(iStream);
Error logs :
Exception
at com.ibm.ejs.jms.listener.MDBWrapper$PriviledgedOnMessage.run(MDBWrapper.java:302)
at java.security.AccessController.doPrivileged(AccessController.java:192)
at com.ibm.ws.security.util.AccessController.doPrivileged(AccessController.java:65)
at com.ibm.ejs.jms.listener.MDBWrapper.callOnMessage(MDBWrapper.java:271)
at com.ibm.ejs.jms.listener.MDBWrapper.onMessage(MDBWrapper.java:240)
at com.ibm.mq.jms.MQSession.run(MQSession.java:1695)
at com.ibm.ejs.jms.JMSSessionHandle.run(JMSSessionHandle.java:1040)
at com.ibm.ejs.jms.listener.ServerSession.connectionConsumerOnMessage(ServerSession.java:1031)
at com.ibm.ejs.jms.listener.ServerSession.onMessage(ServerSession.java:711)
at com.ibm.ejs.jms.listener.ServerSession.dispatch(ServerSession.java:678)
at sun.reflect.GeneratedMethodAccessor34.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:619)
at com.ibm.ejs.jms.listener.ServerSessionDispatcher.dispatch(ServerSessionDispatcher.java:44)
at com.ibm.ejs.container.MDBWrapper.onMessage(MDBWrapper.java:100)
at com.ibm.ejs.container.MDBWrapper.onMessage(MDBWrapper.java:136)
at com.ibm.ejs.jms.listener.ServerSession.run(ServerSession.java:536)
at com.ibm.ws.util.ThreadPool$Worker.run(ThreadPool.java:1497)
Caused by: java.lang.ArrayIndexOutOfBoundsException
at org.apache.xerces.impl.xs.opti.SchemaDOM.endElement(Unknown Source)
at org.apache.xerces.impl.xs.opti.SchemaDOMParser.endElement(Unknown Source)
at org.apache.xerces.impl.xs.traversers.SchemaContentHandler.endElement(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.apache.xerces.impl.xs.traversers.XSDHandler.parseSchema(Unknown Source)
at org.apache.xerces.impl.xs.XMLSchemaLoader.loadSchema(Unknown Source)
at org.apache.xerces.impl.xs.XMLSchemaLoader.loadGrammar(Unknown Source)
at org.apache.xerces.impl.xs.XMLSchemaLoader.loadGrammar(Unknown Source)
at org.apache.xerces.jaxp.validation.XMLSchemaFactory.newSchema(Unknown Source)
at javax.xml.validation.SchemaFactory.newSchema(Unknown Source)
... 24 more