If you're having rendering issues with your jfx 3D boxes all showing up and having weird visibility through the middle, it's because JavaFx isn't able to recognize which object is in fornt of the others, and that's an issue with the "depth buffer" when setting the scene.
To fix this: When you create your scene, you need to set the depthBuffer to true in the fourth parameter. By default it's false which is why JFX doesn't know what to do with the multiple object rendering.
Scene scene = new Scene(group, width, height, true);
(This problem was driving my group INSANE, so I hope it helps if anyone else is having the same problem)