ADDITIONAL SYSTEM INFORMATION :
Java:
openjdk version "11" 2018-09-25
OpenJDK Runtime Environment 18.9 (build 11+28)
OpenJDK 64-Bit Server VM 18.9 (build 11+28, mixed mode)

OS: elementary OS 5.0 Juno (Ubuntu 18.04 LTS)
JavaFX Version: 12-ea+4


A DESCRIPTION OF THE PROBLEM :
When rendering a Stage only a small part is actually displayed. Here a screenshot: https://i.stack.imgur.com/iLpeY.png
This seams related to the Window Manager and/or Gtk.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Run the provided code.
On the provided JDK/JavaFX version on elementary OS.

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
The window should be rendered correctly with Controls to resize the window and the right Size.
ACTUAL -
Only a small part of the window actually gets displayed with NO Controls to resize the window.

---------- BEGIN SOURCE ----------
import javafx.application.Application;
import javafx.fxml.FXMLLoader;
import javafx.scene.Scene;
import javafx.scene.layout.AnchorPane;
import javafx.stage.Stage;

import java.io.ByteArrayInputStream;
import java.io.IOException;

public class App extends Application {

    public static void main(String[] args) {
        launch();
    }
    @Override
    public void start(Stage primaryStage) throws IOException {
        FXMLLoader loader = new FXMLLoader();
        AnchorPane pane = loader.load(new ByteArrayInputStream(fxmlContent.getBytes()));
        primaryStage.setScene(new Scene(pane));
        primaryStage.sizeToScene();
        primaryStage.setResizable(false);

        primaryStage.show();
    }
    public static String fxmlContent = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
            "\n" +
            "<?import javafx.scene.control.Label?>\n" +
            "<?import javafx.scene.control.ListView?>\n" +
            "<?import javafx.scene.image.ImageView?>\n" +
            "<?import javafx.scene.layout.AnchorPane?>\n" +
            "<?import javafx.scene.layout.Pane?>\n" +
            "<?import javafx.scene.text.Font?>\n" +
            "\n" +
            "<AnchorPane prefHeight=\"450.0\" prefWidth=\"650.0\" xmlns=\"http://javafx.com/javafx/10.0.1\" xmlns:fx=\"http://javafx.com/fxml/1\">\n" +
            " <children>\n" +
            " <Pane layoutX=\"234.0\" prefHeight=\"450.0\" prefWidth=\"650.0\" AnchorPane.bottomAnchor=\"0.0\" AnchorPane.leftAnchor=\"0.0\" AnchorPane.rightAnchor=\"0.0\" AnchorPane.topAnchor=\"0.0\">\n" +
            " <children>\n" +
            " <ListView fx:id=\"projectsList\" prefHeight=\"450.0\" prefWidth=\"235.0\" />\n" +
            " <ImageView fx:id=\"iconImage\" fitHeight=\"150.0\" fitWidth=\"148.0\" layoutX=\"367.0\" layoutY=\"31.0\" pickOnBounds=\"true\" preserveRatio=\"true\" />\n" +
            " <Label fx:id=\"createNewProject\" layoutX=\"366.0\" layoutY=\"181.0\" text=\"Label 1\">\n" +
            " <font>\n" +
            " <Font size=\"18.0\" />\n" +
            " </font></Label>\n" +
            " <Label fx:id=\"importProject\" layoutX=\"414.0\" layoutY=\"208.0\" text=\"Label 2\">\n" +
            " <font>\n" +
            " <Font size=\"18.0\" />\n" +
            " </font></Label>\n" +
            " <Label fx:id=\"settings\" layoutX=\"409.0\" layoutY=\"235.0\" text=\"Label 3\">\n" +
            " <font>\n" +
            " <Font size=\"18.0\" />\n" +
            " </font>\n" +
            " </Label>\n" +
            " <Label fx:id=\"versionLabel\" layoutX=\"245.0\" layoutY=\"419.0\" prefHeight=\"17.0\" prefWidth=\"391.0\" text=\"\" />\n" +
            " <Label fx:id=\"aboutLabel\" layoutX=\"245.0\" layoutY=\"401.0\" text=\"Label 4\">\n" +
            " <font>\n" +
            " <Font size=\"14.0\" />\n" +
            " </font>\n" +
            " </Label>\n" +
            " </children>\n" +
            " </Pane>\n" +
            " </children>\n" +
            "</AnchorPane>\n";
}

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

CUSTOMER SUBMITTED WORKAROUND :
A half way working solution is to call: stage.initStyle(StageStyle.UNDECORATED), since that does not require the window is rendered correctly, but without Controls to resize.

The only completely working method i was able to find is to set the JVM option -Djdk.gtk.version=2

FREQUENCY : always