FULL PRODUCT VERSION :
java version "1.8.0_66"
Java(TM) SE Runtime Environment (build 1.8.0_66-b17)
Java HotSpot(TM) 64-Bit Server VM (build 25.66-b17, mixed mode)

ADDITIONAL OS VERSION INFORMATION :
Microsoft Windows [version 10.0.10586]

A DESCRIPTION OF THE PROBLEM :
When you create a WINDOW_MODAL dialog while it's owner-window is minimized, and you then restore the owner window (click on task bar icon), the owner window pops up, but the dialog remains invisible (probably hidden behind it or still minimized)

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
1. Create a scene containing at least two focusable controls (such as a TextFields for instance)
2. Set it as root for a new stage (Application's primaryStage for instance)
3.a. Add a handler for WindowEvent.ON_CLOSE_REQUEST on that stage
3.b. In this handler, make an Alert, set it's modality to WINDOW_MODAL and its owner as the stage, call its showAndWait() method
4. Launch application, minimize the main window, right-click its taskbar icon, and select "Close Window"
5. Restore the main window by clicking its icon on task bar : its frozen. You can't get focus into the TextField, can't minimize, maximize or close it
6. Press ESCAPE: window unfrozen (the alert has been closed)



EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
The dialog should pop up in front of the owner window when it's restored, so you could read and close it and get back control over your application
ACTUAL -
The dialog is invisible, and the owner window is frozen: you can't get focus into the TextField, can't minimize, maximize or close it

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
package application;
	
import javafx.application.Application;
import javafx.geometry.Pos;
import javafx.scene.Scene;
import javafx.scene.control.Alert;
import javafx.scene.control.Alert.AlertType;
import javafx.scene.control.ButtonType;
import javafx.scene.control.TextField;
import javafx.scene.layout.BorderPane;
import javafx.scene.layout.VBox;
import javafx.stage.Modality;
import javafx.stage.Stage;
import javafx.stage.WindowEvent;


public class Main extends Application {
	@Override
	public void start(Stage primaryStage) {
		try {
			BorderPane root = new BorderPane();
			TextField tf1 = new TextField();
			tf1.setPrefColumnCount(10);
			TextField tf2 = new TextField();
			tf2.setPrefColumnCount(10);
			VBox vb = new VBox(4, tf1, tf2);
			vb.setFillWidth(false);
			vb.setAlignment(Pos.CENTER);
			root.setCenter(vb);
			Scene scene = new Scene(root,400,400);
			scene.getStylesheets().add(getClass().getResource("application.css").toExternalForm());
			primaryStage.setScene(scene);
			
			primaryStage.addEventHandler(WindowEvent.WINDOW_CLOSE_REQUEST, (event) -> {
				Alert alert = new Alert(AlertType.INFORMATION, "Close window ?", ButtonType.YES, ButtonType.NO);
				alert.initModality(Modality.WINDOW_MODAL);
				alert.initOwner(primaryStage);
				alert.showAndWait().ifPresent((result) -> {
					if (result == ButtonType.NO)
						event.consume();
				});
			});
			
			primaryStage.show();
		} catch(Exception e) {
			e.printStackTrace();
		}
	}
	
	public static void main(String[] args) {
		launch(args);
	}
}

---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
Press ENTER or ESCAPE on the keyboard when restored owner window is in front : this closes the dialog.