You need to add dir to the junit task. e.g.
<junit dir="${project.working.directory}" ...
Where the directory depends on the project type:
<!-- Initialize properties that depend on build type (build or install) with values unique to applications -->
<target name="set_application_build_properties" depends="load.properties" if="is.wo.app" >
<property name="build.product.dir" value="${dest.dir}${file.separator}${build.app.name}.woa"/>
<property name="installed.product.dir" value="${install.dir}${file.separator}${build.app.name}.woa"/>
<property name="project.working.directory" value="${build.product.dir}"/>
<property name="project.java.dir" value="${build.product.dir}${file.separator}Contents${file.separator}Resources${file.separator}Java"/>
</target>
<!-- Initialize properties that depend on build type (build or install) with values unique to frameworks -->
<target name="set_framework_build_properties" depends="load.properties" if="is.wo.framework" >
<property name="build.product.dir" value="${dest.dir}${file.separator}${project.name}.framework"/>
<property name="installed.product.dir" value="${install.dir}${file.separator}${project.name}.framework"/>
<!-- Use the installed location as that will be populated for regular and install builds -->
<property name="project.working.directory" value="${install.dir}${file.separator}${project.name}.framework${file.separator}Resources${file.separator}Java"/>
<property name="project.java.dir" value="${project.working.directory}"/>
</target>