Run attached code:

import javafx.application.Application;
import javafx.scene.Group;
import javafx.scene.Scene;
import javafx.stage.Stage;

public class CoordinatesIssue extends Application {

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

    @Override
    public void start(final Stage stage) throws Exception {
        stage.setX(0);
        prepareSourceStage(stage);

        Stage stageTarget = new Stage();
        stageTarget.setX(600);
        prepareTargetStage(stageTarget);
    }

    private void prepareTargetStage(Stage stageTarget) {
        stageTarget.setScene(new Scene(new Group(), 700, 700));
        stageTarget.show();
    }

    private void prepareSourceStage(final Stage stage) {
        stage.setScene(new Scene(new Group(), 600, 700));
        stage.show();
    }
}

I see both scenes in a such way, so their right borders are the same as the right border of the screen size.