Yes, there's a problem with your XML file:
Caused by: com.sun.org.apache.xerces.internal.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
at com.sun.org.apache.xerces.internal.impl.io.UTF8Reader.invalidByte(Unknown Source)
at com.sun.org.apache.xerces.internal.impl.io.UTF8Reader.read(Unknown Source)
at javax.xml.parsers.DocumentBuilder.parse(Unknown Source)
the problem is at byte position 3331 (line 66): <perMill>�</perMill>
You can see this if you open it with SC UniPad, configured not to suppress load errors
Having fixed that, I see: "line 1:149 mismatched input '<EOF>' expecting LPAR" multiple times. I haven't seen that before, but it'd be from XPathEnhancerParser; possibly it doesn't like the full stop (period) characters in your xpaths? Output is produced, so it might not matter, but still, it would be good to understand/fix.
For what it is worth, I used Docx4J.FLAG_NONE (which you need to process repeats), and today's nightly, which contains a relevant fix: http://www.docx4java.org/docx4j/docx4j- ... 130823.jar