Changing scenes with Alert JavaFX

Question

I'm using JavaFX and trying to make a small GUI application where the user can interact with spacetraders.io API. I've implemented an Alert dialog box when the user attempts to make any transaction (purchase a ship, obtain a loan, purchase goods, sell goods...), and once the user has confirmed their transaction, the stage will be switched to a stage that displays the results of the transaction when shown.

Correct Display

The Alert dialog box functions fine but the switching of stage presents an issue. When I switch the stage, the full scene is not loaded for some odd reason, the back button is chopped off.

Chopped Off Display

When I then click anywhere on the window, the stage is fully shown as in the first image. (all it takes is one click anywhere inside the window).

When I remove the Alert, the stage loads fine. But when I put the same code into an ifPresent lambda, the stage fails to load fully/properly.

Alert alert = new Alert(Alert.AlertType.CONFIRMATION, "Are you sure you want to obtain this loan?");
alert.showAndWait().ifPresent(response -> {
    if (response == ButtonType.OK) {
        BorderPane borderPane = new BorderPane();
        //make title, backbtn, res
        borderPane.setTop(title);
        borderPane.setBottom(backBtn);
        borderPane.setCenter(res);
        Scene scene = new Scene(borderPane, 600, 400);
        primaryStage.setScene(scene);
        primaryStage.show();
        event.consume();
    }
});

I've looked at the docs and I can't seem to figure out why this is the case? Any solutions are welcome?