Logger is set to OFF after thread.join()

I have a launcher class with shutdownHook thread in main method:

Runtime.getRuntime().addShutdownHook(new Thread() {
public void run() {
try

{ logger.info("transefer server is stopping"); controller.stop(); }

catch (Throwable e) {
logger.warn("something goes wrong when stopping transfer Server:\n{}",
Throwables.getStackTraceAsString(e));
} finally

{ logger.info("transfer server is down."); }

}

});

In controller to stop the server, I did things below:
public void stop() {
if (transferServer.isStart())

{ transferServer.stop(); }

logger.info("Server is down");
}

and in server, I stop instances like this:
public void stop() {
if (isStart()) {
running = false;

for (Map.Entry<String, TransferInstanceInterface> entry : transferInstances.entrySet()) {
TransferInstanceInterface instance = entry.getValue();
if (instance.isStart())

{ instance.stop(); }

}
logger.info("Transfer server stopped");
}
}

and in instance I stop two thread:
public void stop() {
logger.info("Transfer instance[" + name + "] is stopping...");

if (messageListener.isStart())

{ messageListener.stop(); }

if (messageProcessor.isStart())

{ messageProcessor.stop(); }

running = false;
logger.info("Transfer instance[" + name + "] is down.");
}

for messageListener, I stopped is like this:
public void stop() {
logger.info("Message listener for topic[" + topic + "] is stopping...");

try {
if (running) {
running = false;
if (null != consumer)

{ consumer.close(); }

thread.join();
logger.info("Message listener for topic[" + topic + "] is down.");
}
} catch (InterruptedException e)

{ logger.error(e.getMessage()); }

}

seems that after thread.join(), all the loggers are set to level off, and won't produce any log.
What the right way to make logger produce log entries after thread.join()?