Given that you're using MMX 5.5.4, you may want to take this issue to Red Hat Support (GSS). They can help you with product support issues.
Regarding the current issue, modeling via the Web Service to Relational approach is tricky. The import wizard will build a model based on the WSDL but the quality of the model depends on the quality of the WSDL. Also understanding how to write a query against is a bit unintuitive. The XML-Relational Connectors doc provides good background information on this.