The hadoop.root.logger defined in log4j.properties is only used by applications. The scripts (bin and daemons) always set it to HADOOP_ROOT_LOGGER or "INFO,console" so the installed log4j.properties appears to be ignored. The wiki doesn't cover this:
We should update the cluster setup docs to indicate how the loglevel is configured and also add a comment in log4j.properties that the hadoop.root.logger defined there is not used by Hadoop itself, that HADOOP_ROOT_LOGGER must be set. This is relevant for commands and daemons, though the latter also has daemonlog (http://hadoop.apache.org/common/docs/current/commands_manual.html#daemonlog).