FULL PRODUCT VERSION :
java version "1.8.0_66"
Java(TM) SE Runtime Environment (build 1.8.0_66-b17)
Java HotSpot(TM) 64-Bit Server VM (build 25.66-b17, mixed mode)

ADDITIONAL OS VERSION INFORMATION :
Microsoft Windows [Version 6.1.7601]

A DESCRIPTION OF THE PROBLEM :
Since Java8u60, semi-transparent 3D-shapes are supported, without full support of z-depth considerations. With some emphasis on the scene graph order, that is a very important and helpful feature for many use cases.

But: 3D-shapes with a semi-transparent diffuse color are rendered with strange effects or blend mode.

However, working with an equivalent colored semi-transparent texture combined with a diffuse fully opaque white color works fine as expected.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Open the attached FXML file with your demo\javafx_samples\3DViewer, and look at the line of 7 spheres rendered with colors with different alphas, and the 2 spheres below rendered with semi-transparent textures for comparison. For the comparison, you need two image files:
red.png filled with rgba #ff7f7fff
redtrans.png filled with rgba #ff7f7f33

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
The 7 spheres should be renderd like the second sphere from the second line. 
ACTUAL -
On a black background, the transparency of the 7 spheres is totally ignored. On a white background, the transparency is reflected with some strange blending effects. When the spheres are rendered on top of each other, the blending is also quite strange. 

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
<?xml version="1.0" encoding="UTF-8"?>

<?import java.lang.*?>
<?import javafx.scene.*?>
<?import javafx.scene.shape.*?>
<?import javafx.scene.image.Image?>
<?import javafx.scene.paint.Color?>
<?import javafx.scene.paint.PhongMaterial?>

<Group xmlns="http://javafx.com/javafx/8" xmlns:fx="http://javafx.com/fxml/1">
   <children>
    <Sphere translateX="-5.0">
	<material>
        <PhongMaterial>
            <diffuseColor>
                <Color red="1.0" green="0.5" blue="0.5" opacity="1.0"/>
            </diffuseColor>
        </PhongMaterial>
    </material>
    </Sphere>
    <Sphere translateX="-3.0">
	<material>
        <PhongMaterial>
            <diffuseColor>
                <Color red="1.0" green="0.5" blue="0.5" opacity="0.5"/>
            </diffuseColor>
        </PhongMaterial>
    </material>
    </Sphere>
    <Sphere translateX="-1.0">
	<material>
        <PhongMaterial>
            <diffuseColor>
                <Color red="1.0" green="0.5" blue="0.5" opacity="0.3"/>
            </diffuseColor>
        </PhongMaterial>
    </material>
    </Sphere>
    <Sphere translateX="1.0">
	<material>
        <PhongMaterial>
            <diffuseColor>
                <Color red="1.0" green="0.5" blue="0.5" opacity="0.2"/>
            </diffuseColor>
        </PhongMaterial>
    </material>
    </Sphere>
    <Sphere translateX="3.0">
	<material>
        <PhongMaterial>
            <diffuseColor>
                <Color red="1.0" green="0.5" blue="0.5" opacity="0.1"/>
            </diffuseColor>
        </PhongMaterial>
    </material>
    </Sphere>
    <Sphere translateX="5.0">
	<material>
        <PhongMaterial>
            <diffuseColor>
                <Color red="1.0" green="0.5" blue="0.5" opacity="0.05"/>
            </diffuseColor>
        </PhongMaterial>
    </material>
    </Sphere>
    <Sphere translateX="7.0">
	<material>
        <PhongMaterial>
            <diffuseColor>
                <Color red="1.0" green="0.5" blue="0.5" opacity="0.0"/>
            </diffuseColor>
        </PhongMaterial>
    </material>
    </Sphere>

    <Sphere translateX="-5.0" translateY="2.0">
	<material>
        <PhongMaterial>
            <diffuseColor>
                <Color red="1.0" green="1.0" blue="1.0" opacity="1.0"/>
            </diffuseColor>
			<diffuseMap>
				<Image url="@red.png"/> <!-- image with color #ff7f7fff -->
			</diffuseMap>
        </PhongMaterial>
    </material>
    </Sphere>
    <Sphere translateX="1.0" translateY="2.0">
	<material>
        <PhongMaterial>
            <diffuseColor>
                <Color red="1.0" green="1.0" blue="1.0" opacity="1.0"/>
            </diffuseColor>
			<diffuseMap>
				<Image url="@redtrans.png"/> <!-- image with color #ff7f7f33 -->
			</diffuseMap>
        </PhongMaterial>
    </material>
    </Sphere>

   </children>
</Group>

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

CUSTOMER SUBMITTED WORKAROUND :
For static coloring, textures might be used for all semi-transparent 3D shapes as a workaround. However, this works not for dynamic coloring, e.g. fading 3D shapes in or out or changing the color of semi-transparent 3D shapes.