Here's out ant task which runs fine from Eclipse under Hibernate 3.1.2
Code:
<target name="hbm2java" description="Generate .java from .hbm files.">
  <delete>
    <fileset dir="${hibernateDO.dir}">
      <include name="**/*.java"/>            
    </fileset>         
  </delete>
      
  <taskdef name="hibernatetool" classname="org.hibernate.tool.ant.HibernateToolTask">
    <classpath refid="classpath.common"/>
  </taskdef>
      
  <hibernatetool destdir="${src.dir}">
    <configuration>
      <fileset dir="${src.dir}">
        <include name="**/hbm/*.hbm.xml"/>
      </fileset>
    </configuration>
    <hbm2java generics="false"/>
  </hibernatetool>
</target>
Don't forget to rate if this helps :-)