In case of problems with service configuration, it's important to know from which JAR/WAR it comes. For that purpose, the JVM system property org.exoplatform.container.configuration.debug can be used.

java -Dorg.exoplatform.container.configuration.debug ...

If the property is enabled, the container configuration manager will log the configuration adding process at INFO level.

......
   Add configuration jar:file:/D:/Projects/eXo/dev/exo-working/exo-tomcat/lib/exo.kernel.container-trunk.jar!/conf/portal/configuration.xml
   Add configuration jar:file:/D:/Projects/eXo/dev/exo-working/exo-tomcat/lib/exo.kernel.component.cache-trunk.jar!/conf/portal/configuration.xml
   Add configuration jndi:/localhost/portal/WEB-INF/conf/configuration.xml
        import jndi:/localhost/portal/WEB-INF/conf/common/common-configuration.xml
        import jndi:/localhost/portal/WEB-INF/conf/database/database-configuration.xml
        import jndi:/localhost/portal/WEB-INF/conf/ecm/jcr-component-plugins-configuration.xml
        import jndi:/localhost/portal/WEB-INF/conf/jcr/jcr-configuration.xml 
   ......