Java GUI Thread not closing

Question

I have a plugin for an application containing a GUI (Swing) and is started as a thread. The GUI starts a thread that does some processing on a buttonevent, right after disposing itself. While processing, a dialog window functions as a logger. Everything works fine, the GUI and dialog window will close and the threads terminate, when calling window.dispose() after the processing finished. Threads are started as Threads, not via SwingUtilities (I tried many times, but i just can't get that to work).

Basicly the entry class for the application:

public void calledByApplication(){
     RunnableClass.startGui(this);
}

public void doStuff(){         //GUI actually gets created here
     gui.setVisible(true);
}

public void calledWhenSaveButtonPressed(){
    //Process some stuff
    gui.dispose();             //works, thread terminates
}

RunnableClass (implements Runnable):

ApplicationEntryClass aec;

public RunnableClass(ApplicationEntryClass aec){
    this.aec = aec;
}

public void run(){
    aec.doStuff();
}

public static void startGui(ApplicationEntryClass aec){
    Thread guiThread = new Thread(new RunnableClass(aec));
    guiThread.start();
}

Gui Class:

public void calledWhenSaveButtonPressed(){
    aec.calledWhenSaveButtonPressed();
}

public void calledWhenCancelButtonPressed(){
    this.dispose();           //doesn't work
}

My problem: When trying to dispose the GUI via button event (or the x with JFrame.DISPOSE_ON_CLOSE), it closes, but the thread doesn't terminate. After looking at the stack i noticed, that the EventDispatchThread gets stuck on EventDispatchThread.pumpEventForFilter(...).

I'm well aware, that the issue could be, that the thread doesn't get automatically destroyed. But since i'm new to threading i don't really know where to start troubleshooting. Any suggestions?

Edit: The dialog window is not the problem. Also, i can't use System.exit() or else the application calling the plugin will terminate.