Starting with 8u40 early release (build 23), the rendering of textured 3D nodes overlaping other nodes differs from previous releases, up to 8u31.

Before 8u40 : the polygons rendered behind the transparent one are visible with their own color

After 8u40 : the polygons rendered behind the transparent one are visible with a default color (scene background probably)

I suspect a z-buffer issue here...

I copy here a SSCE to illustrate the problem. I tested it against 8u25 8u31 8u40 and 9, as one can see on joined screenshots.

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import java.awt.BasicStroke;
import java.awt.Graphics2D;
import java.awt.image.BufferedImage;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.util.Map.Entry;
import java.util.TreeMap;

import javafx.application.Application;
import javafx.scene.Group;
import javafx.scene.PerspectiveCamera;
import javafx.scene.Scene;
import javafx.scene.SceneAntialiasing;
import javafx.scene.control.Label;
import javafx.scene.image.Image;
import javafx.scene.paint.Color;
import javafx.scene.paint.PhongMaterial;
import javafx.scene.shape.Box;
import javafx.scene.transform.Rotate;
import javafx.scene.transform.Translate;
import javafx.stage.Stage;

import javax.imageio.ImageIO;

public class TransparencyBug extends Application {

	@Override
	public void start(Stage stage) throws Exception {
		final TreeMap<Object, Object> props = new TreeMap<>(System.getProperties());
		for (Entry<Object, Object> entry : props.entrySet()) {
			System.out.println(entry);
		}

		final BufferedImage awtImage = new BufferedImage(100, 100, BufferedImage.TYPE_INT_ARGB);
		final Graphics2D g = (Graphics2D) awtImage.getGraphics();
		g.setColor(java.awt.Color.WHITE);
		g.setStroke(new BasicStroke(20));
		g.drawLine(-20, -20, 120, 120);
		g.drawLine(-20, 120, 120, -20);
		final ByteArrayOutputStream imageData = new ByteArrayOutputStream();
		ImageIO.write(awtImage, "png", imageData);
		final Image fxImage = new Image(new ByteArrayInputStream(imageData.toByteArray()));

		final Box box1 = new Box(200, 200, 200);
		box1.setMaterial(new PhongMaterial(Color.RED));
		final Box box2 = new Box(100, 100, 100);
		final PhongMaterial material = new PhongMaterial();
		material.setDiffuseMap(fxImage);
		box2.setMaterial(material);
		box2.getTransforms().add(new Translate(0, 20, -130));
		final Label label = new Label(System.getProperty("java.vendor") + "\nJava v."
				+ System.getProperty("java.runtime.version") + "\nFX v." + System.getProperty("javafx.runtime.version"));
		label.getTransforms().add(new Translate(-95, -95, -100.1));
		final Group group = new Group();
		group.getTransforms().add(new Translate(350, 250));
		group.getChildren().addAll(box1, box2, label);
		final Scene scene = new Scene(group, 600, 600, true, SceneAntialiasing.BALANCED);
		scene.setCamera(new PerspectiveCamera());
		scene.getCamera().getTransforms().addAll(new Rotate(-15, Rotate.Y_AXIS), new Rotate(-10, Rotate.X_AXIS));
		stage.setScene(scene);
		stage.show();
	}

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

}