Program: 62433
Project: 62433
Buggy source:
private void startApp(Stage stage) throws Throwable {
  FXMLLoader parentLoader=new FXMLLoader();
  FXMLLoader tablePopupLoader=new FXMLLoader();
  context=SpringApplication.run(SpringAppConfig.class);
  tablePopupLoader.setControllerFactory(context::getBean);
  parentLoader.setControllerFactory(context::getBean);
  AnchorPane tableAnchor=tablePopupLoader.load(getClass().getResourceAsStream("String_Node_Str"));
  Parent root=parentLoader.load(getClass().getResourceAsStream("String_Node_Str"));
  controller=parentLoader.getController();
  HostServicesDelegate hostServices=HostServicesFactory.getInstance(this);
  controller.setHostServices(hostServices);
  Scene scene=new Scene(root);
  scene.getStylesheets().add("String_Node_Str");
  Rectangle2D bounds=Screen.getPrimary().getVisualBounds();
  stage.setWidth(bounds.getWidth());
  stage.setHeight(bounds.getHeight());
  stage.setX(0);
  stage.setY(0);
  stage.setTitle("String_Node_Str");
  stage.getIcons().add(new Image(getClass().getResourceAsStream("String_Node_Str")));
  Stage tableStage=new Stage();
  tableStage.setScene(new Scene(tableAnchor));
  tableStage.setTitle("String_Node_Str");
  tableStage.initModality(Modality.WINDOW_MODAL);
  tableStage.initOwner(scene.getWindow());
  tableStage.getIcons().add(new Image(getClass().getResourceAsStream("String_Node_Str")));
  controller.setStage(stage);
  controller.setScene(scene);
  controller.setTableAnchor(tableAnchor);
  controller.setTableStage(tableStage);
  stage.setScene(scene);
  stage.show();
  scene.getAccelerators().put(new KeyCodeCombination(KeyCode.S,CONTROL_DOWN),controller::saveDoc);
  scene.getAccelerators().put(new KeyCodeCombination(KeyCode.N,CONTROL_DOWN),() -> {
    controller.newDoc(null);
  }
);
}

Fixed version (ground truth):
private void startApp(Stage stage) throws Throwable {
  FXMLLoader parentLoader=new FXMLLoader();
  FXMLLoader tablePopupLoader=new FXMLLoader();
  context=SpringApplication.run(SpringAppConfig.class);
  tablePopupLoader.setControllerFactory(context::getBean);
  parentLoader.setControllerFactory(context::getBean);
  AnchorPane tableAnchor=tablePopupLoader.load(getClass().getResourceAsStream("String_Node_Str"));
  Parent root=parentLoader.load(getClass().getResourceAsStream("String_Node_Str"));
  controller=parentLoader.getController();
  HostServicesDelegate hostServices=HostServicesFactory.getInstance(this);
  controller.setHostServices(hostServices);
  Scene scene=new Scene(root);
  scene.getStylesheets().add("String_Node_Str");
  Rectangle2D bounds=Screen.getPrimary().getVisualBounds();
  stage.setWidth(bounds.getWidth());
  stage.setHeight(bounds.getHeight());
  stage.setX(0);
  stage.setY(0);
  stage.setTitle("String_Node_Str");
  stage.getIcons().add(new Image(getClass().getResourceAsStream("String_Node_Str")));
  Stage tableStage=new Stage();
  tableStage.setScene(new Scene(tableAnchor));
  tableStage.setTitle("String_Node_Str");
  tableStage.initModality(Modality.WINDOW_MODAL);
  tableStage.initOwner(scene.getWindow());
  tableStage.getIcons().add(new Image(getClass().getResourceAsStream("String_Node_Str")));
  controller.setStage(stage);
  controller.setScene(scene);
  controller.setTableAnchor(tableAnchor);
  controller.setTableStage(tableStage);
  stage.setScene(scene);
  stage.show();
  scene.getAccelerators().put(new KeyCodeCombination(KeyCode.S,SHORTCUT_DOWN),controller::saveDoc);
  scene.getAccelerators().put(new KeyCodeCombination(KeyCode.N,SHORTCUT_DOWN),() -> {
    controller.newDoc(null);
  }
);
}