When running the attached SSCCE with Java 8u45 we get an additional taskbar entry for the new window (screenshot -> http://i.imgur.com/0G4JRhs.png).

When we run the same example with Java 7 we don't get this additonal taskbar entry (screenshot -> http://i.imgur.com/frjivcT.png).

We don't get the additonal taskbar entry in Windows regardless of the Java version.

We expect that additional APPLICATION_MODAL stage windows behave the same across all operating systems with regard to the display of taskbar icons.

Example code:

import javafx.application.Application;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.geometry.Insets;
import javafx.geometry.Pos;
import javafx.scene.Node;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.layout.HBox;
import javafx.scene.paint.Color;
import javafx.stage.Modality;
import javafx.stage.Stage;
import javafx.stage.StageStyle;
import javafx.stage.Window;

public class Main extends Application {

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

    @Override
    public void start(final Stage primaryStage) throws Exception {
        Button openDialogBtn = new Button("Open dialog");
        openDialogBtn.setOnAction(new EventHandler<ActionEvent>() {
            @Override
            public void handle(final ActionEvent event) {
                openDialog(primaryStage);
            }
        });

        HBox root = createRoot(Pos.CENTER, openDialogBtn);

        primaryStage.setScene(new Scene(root, 300, 50, Color.BLUE));
        primaryStage.setTitle("Stage Examples");
        primaryStage.show();
    }

    private HBox createRoot(final Pos pos, final Node... nodes) {
        HBox root = new HBox(10);
        root.getChildren().addAll(nodes);
        root.setPadding(new Insets(10));
        root.setAlignment(pos);
        return root;
    }

    private void openDialog(final Window owner) {
        final Stage stage = new Stage(StageStyle.TRANSPARENT);
        Button close = new Button("Close dialog");
        close.setOnAction(new EventHandler<ActionEvent>() {
            @Override
            public void handle(final ActionEvent event) {
                stage.close();
            }
        });

        HBox root = createRoot(Pos.BOTTOM_CENTER, close);
        root.setStyle("-fx-border-width: 2px; -fx-border-color: #f00");

        stage.setScene(new Scene(root, 200, 200, Color.TRANSPARENT));
        stage.initOwner(owner);
        stage.initModality(Modality.APPLICATION_MODAL);
        stage.show();
    }
}

Thanks!