Rotating any shape on any 3D axis results in a truncated scene view. Below is a simple example that illustrates this bug.  We should see a 4 sided polygon, but we only see a triangle instead.

import javafx.application.Application;
import javafx.geometry.Point3D;
import javafx.scene.Group;
import javafx.scene.Scene;
import javafx.scene.shape.Polygon;
import javafx.scene.transform.Rotate;
import javafx.scene.transform.Translate;
import javafx.stage.Stage;

public class RotationBug extends Application {
   @Override
   public void start(Stage stage) throws Exception {
      Group g = new Group();
      Scene scene = new Scene(g, 400, 400);
      Polygon p = new Polygon(new double[] { 0, 0, 0, 100, 100, 100, 100, 0, 0, 0 });
      p.setStrokeWidth(5);
      p.getTransforms().add(new Translate(200, 200));
      p.getTransforms().add(new Rotate(45, 0, 0, 0, new Point3D(1, 1, 0)));
      g.getChildren().add(p);
      stage.setScene(scene);
      stage.setVisible(true);
   }
   public static void main(String[] args) {
      Application.launch(RotationBug.class, args);
   }
}