ADDITIONAL SYSTEM INFORMATION :
Ubuntu 22.04 (no issue on Windows 10 / latest MacOS)

A DESCRIPTION OF THE PROBLEM :
On linux, after modal stage is closed, focus is returned to primary stage, but event handlers (like mouse hovering) doesn't work.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
1. launch app
2. click on button to open modal window
3. *After clicking to button move mouse a little left/right (to not hovering over modal window)*
4. await for timer to tick and modal stage is closed
5. hover over button - no printlns executed

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
same behavior as on Windows and MacOS: mouse events delivered to primary stage
ACTUAL -
mouse events aren't delivered to primary stage

---------- BEGIN SOURCE ----------
import javafx.application.Application;
import javafx.application.Platform;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.layout.StackPane;
import javafx.stage.Modality;
import javafx.stage.Stage;

import java.util.Timer;
import java.util.TimerTask;

class TestApplication extends Application {
    @Override
    public void start(Stage primaryStage) {
        var timer = new Timer();
        primaryStage.setTitle("Primary stage");
        var button = new Button();
        button.setText("Open modal");
        button.setOnMouseEntered(event -> System.out.println("ENTER: " + event));
        button.setOnMouseExited(event -> System.out.println("EXIT: " + event));

        button.setOnAction(event -> {
            System.out.println("ACTION: " + event);

            var modalStage = new Stage();
            modalStage.setTitle("Modal stage");
            modalStage.initModality(Modality.WINDOW_MODAL);
            modalStage.initOwner(primaryStage);
            modalStage.setScene(new Scene(new StackPane(), 100.0, 100.0));
            modalStage.show();
            timer.schedule(new TimerTask() {
                @Override
                public void run() {
                    System.out.println("TIMED OUT!");
                    Platform.runLater(modalStage::close);
                }
            }, 2000);
        });
        primaryStage.setScene(new Scene(new StackPane(button), 500.0, 500.0));
        primaryStage.show();
    }

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

CUSTOMER SUBMITTED WORKAROUND :
1. use Modality.NONE - not fully a workaround, as behavior is different
2. move mouse out of window and return it back after modal stage is closed
3. click into window after modal stage is closed

FREQUENCY : always