Did you create a new milestone in the JavaFX Application Thread?
Try the following:
javafx.application.Platform.runLater(new Runnable() { @Override public void run() { Stage stage = new Stage(); stage.setScene(new Scene(new Group(new Button("my second window")))); stage.show(); } });
All operations with the FX interface must be performed in the JavaFX Application Theme section, see http://docs.oracle.com/javafx/2/architecture/jfxpub-architecture.htm#sthref8
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