ADDITIONAL SYSTEM INFORMATION :
DELL OPTIPLEX 7010
Ubuntu 18.04 amd64
JDK 1.8.0_191

A DESCRIPTION OF THE PROBLEM :
When repeating PopupControl.show and hide, XID collision messages appear. Attached the simple program that reproduces the issue.

I know a similar issue has been reported in other OSS project; https://bugs.freedesktop.org/show_bug.cgi?id=21583. But I think that this issue should be tracked, in order to clarify where the root cause of this particular issue is and provide a workaround if possible.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
1) Compile sample/Main.java and sample/PopupTest.java
   % javac -d . sample/*java
2) Run sample.Main
   % java sample.Main
3) Click the button and wait for a while

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
No warning message is shown.
ACTUAL -
The following line is shown a lot of times.

(java:14329): Gdk-WARNING **: 19:35:46.301: XID collision, trouble ahead


---------- BEGIN SOURCE ----------
== sample/Main.java ==
package sample;

import javafx.application.Application;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.scene.Group;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.stage.Stage;
import javafx.stage.Window;

public class Main extends Application {

    PopupTest popup = new PopupTest();

    @Override
    public void start(Stage stage) throws Exception {
        Group root = new Group();
        final Scene scene = new Scene(root);
        scene.getStylesheets().add(Main.class.getResource("style.css").toExternalForm());

        final Button button = new Button("show popup");
        button.setOnAction(new EventHandler<ActionEvent>() {
            @Override
            public void handle(ActionEvent event) {
Window window = scene.getWindow();
                for (int i = 0; i < 100000; i++) {
                    popup.hide();
                    popup.show(window);
                }
            }
        });
        root.getChildren().add(button);
        stage.setScene(scene);
        stage.show();
    }

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

== sample/PopupTest.java ==
package sample;

import javafx.scene.control.Label;
import javafx.scene.control.PopupControl;
import javafx.scene.layout.StackPane;
import javafx.scene.shape.Rectangle;

public class PopupTest extends PopupControl {
    public PopupTest() {
        getStyleClass().add("popup");
        StackPane pane = new StackPane();
        pane.getStyleClass().add("pane");
        Rectangle rectangle = new Rectangle(250, 250);
        rectangle.getStyleClass().add("rect");
        Label text = new Label("popup test");
        text.getStyleClass().add("text");
        pane.getChildren().addAll(rectangle, text);
        getScene().setRoot(pane);
    }
}

== sample/sample.fxml ==
<?import javafx.geometry.Insets?>
<?import javafx.scene.layout.GridPane?>

<?import javafx.scene.control.Button?>
<?import javafx.scene.control.Label?>
<GridPane fx:controller="sample.Controller"
          xmlns:fx="http://javafx.com/fxml" alignment="center" hgap="10" vgap="10">
</GridPane>

== sample/style.css ==
.popup {
    -fx-font-size: 24px;
}

.popup .rect {
    -fx-fill: green;
}

.popup .text {
    -fx-text-fill: white;
    -fx-font-weight: bold;
}
---------- END SOURCE ----------