Facing a similar error. I receive SAXParseException of "org.apache.axis.AxisFault: org.xml.sax.SAXParseException: The markup in the document following the root element must be well-formed." when I run it with Oracle app server 11i. But when I run it as a standalone java program it is working fine. I am using Alfresco Enterprise 3.4.
The above solution mentioned cannot help since I do not have permission to make changes on Oracle server. Pls suggest a solution on Alfresco front asap.