This week's book giveaway is in the OCPJP forum. We're giving away four copies of OCA/OCP Java SE 7 Programmer I & II Study Guide and have Kathy Sierra & Bert Bates on-line! See this thread for details.
Which library are you using for reading doc files - Apache POI? If so, that doesn't support the XML-based Office files yet. You could try the beta version of POI, which does support DOCX to a certain degree.