Issue:
When a Dialog is opened it's not centered to the parent stage, no matter what its size is. When the content of the dialog gets larger, the off-center location gets increased.

Code to reproduce. Click any button to see the issue.

import javafx.application.Application;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.control.ButtonType;
import javafx.scene.control.Dialog;
import javafx.scene.control.Label;
import javafx.scene.layout.BorderPane;
import javafx.scene.layout.VBox;
import javafx.stage.Stage;
import javafx.stage.Window;

public class PopupLocationProblem extends Application {

public static void main(String[] args) {
launch(args);
}

@Override
public void start(Stage primaryStage) throws Exception {
BorderPane center = new BorderPane();
Button showSmallPopup = new Button("Show Small Popup");
showSmallPopup.setOnAction(e -> {
showPopUp(primaryStage, true);
});

Button showBigPopup = new Button("Show Big Popup");
showBigPopup.setOnAction(e -> {
showPopUp(primaryStage, false);
});

VBox buttons = new VBox(showSmallPopup, showBigPopup);

center.setCenter(buttons);

Scene scene = new Scene(center);
primaryStage.setScene(scene);
primaryStage.setWidth(600);
primaryStage.setHeight(400);
primaryStage.show();
}

private void showPopUp(Window owner, boolean small) {
Dialog<ButtonType> d = new Dialog<>();
d.initOwner(owner);
d.setTitle("Bad Centering - " + (small ? "Small" : "Big"));
if (small) {
d.getDialogPane().setContent(new Label("This is short."));
} else {
d.getDialogPane().setContent(new Label("This is a very long message to show how wrongly the popup positions itself when the content is large. The longer you make this text the more wrong it gets."));
}
d.getDialogPane().getButtonTypes().addAll(ButtonType.OK, ButtonType.CANCEL);
d.showAndWait();
}

}