When I use the layer manager and rigify together my feet and hand bones vanish.
1. generate a rigify rig
2. in layer manager set the "all objects on layer to draw wire" beachball button on.
3. toggle draw wire off
4. select rig, enter pose mode. Feet, hands, and finger bones vanish.
The missing bones are still there. You can select them in edit mode or in wireframe view.
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WORKAROUND
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I have found that in pose mode with the missing bone selected (wireframe display) turn on wireframe on the display option under the bone tab, where you assign the custom shape.
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