I used the <zip/> ant task to package the app. It also works the second and all further starts of mule (version 3.1.2 btw)
cli unzip works:
$ unzip ../build/dist/store.zip
Archive: ../build/dist/store.zip
creating: lib/
inflating: lib/groovy-ldap.jar
inflating: lib/spring-ldap-1.3.1.RELEASE-all.jar
inflating: lib/spring-security-ldap-3.0.5.RELEASE.jar
creating: classes/
....
inflating: mule-app.properties
inflating: mule-deploy.properties
inflating: mule-config.xml