Depth testing no longer works on 3D elements on the primaryStage after bringing up a second stage with 2D UI controls.
In order to reproduce this bug, update and run TestViewer:

TestViewer is checked into the gfx-3d-api branch in:
jfx/apps/internal/TestViewer

Note that depth testing does work on the 3D scene on the primaryStage.
To control the camera and observe the 3D scene from various angles:
[*] Alt + LMB (Left Mouse Button) : Orbit the camera
[*] Alt + MMB (Middle Mouse Button) : Track/Pan the camera
[*] Alt + RMB (Right Mouse button) : Zoom the camera

The press "u", which will bring up the second stage with 2D UI controls.
Note that depth testing no longer works on the 3D scene on the primaryStage.

While chatting with Chien, Chien believes that this may be due to a state restore bug somewhere.