log4j2 configuration not being applied when custom class loading

I have a Java application (= launcher) which loads classes via a custom ClassLoader. In my launched application as well as in the launcher I'm using log4j2 with a custom XML configuration.

In the launcher:

private static final Logger LOGGER;

static
{
    loadLog4jConfiguration(ApplicationLauncherClient.class);
    LOGGER = getLogger();
}

loadLog4jConfiguration() is implemented as follows:

public static void loadLog4jConfiguration(final Class<?> clazz)
{
    try
    {
        String resourceName = "launcher-log4j2.xml";
        try (InputStream inputStream = clazz.getResourceAsStream(resourceName))
        {
            if (inputStream == null)
            {
                System.err.println("Cannot find resource: " + resourceName);
            } else
            {
                ConfigurationSource configurationSource = new ConfigurationSource(inputStream);
                Configurator.initialize(null, configurationSource);
            }
        }
    } catch (final Exception exception)
    {
        exception.printStackTrace();
    }
}

In the launched application I do the same setup for log4j2 but I load a *different* log4j2.xml file from the classpath (e.g. to provide JTextArea appending of log messages).

Unfortunately, the JTextArea logs do not work when custom classloading. They work however when I launch the application normally (e.g. via IDE). I assume there is some sort of clash between log4j2 instances. The launcher and the launched application hold the log4j2 maven dependency. How would I resolve this cleanly? I do not want to remove log4j2 from the launcher entirely. I thought about maybe always passing a class instance into the getLogger() constructor on the launched application but that didn't help either. I printed out the ClassLoader of the LOGGER instance on the launched application and it said sun.misc.Launcher$AppClassLoader in both cases (when custom classloading and when launching it normally via the IDE) so now I'm not sure what else to try.