I think there's a typo in VerticalAligment.setXslFO method. It sets superscript as "sup" and that produces the following exception in FOP:
ERROR org.apache.fop.apps.FOUserAgent - Invalid property value encountered in vertical-align="sup": org.apache.fop.fo.expr.PropertyException: null:1:897: No conversion defined sup; property:'vertical-align' (See position 3:120)
According to http://www.w3.org/TR/xsl/#vertical-align possible values are "baseline | middle | sub | super | text-top | text-bottom | <percentage> | <length> | top | bottom | inherit". fop.xsd bundled with docx4j is correct. I'm enclosing patch that fixes this little issue.