Rigify Disappearing Bones

[pi3rc3]

I created a rigify Human and matched the bones with my model and everything looked fine. When I generated the rig it only has the Head, Neck, Shoulders, Chest and Stomach. Is there some important rule i am missing to why it decided too not generate the rest of the rig?
Thanks!

[Richard_Marklew]

Do you get any error message at the top of the blender interface such as

In File / User Preferences / File, have you enabled ‘Auto Run Python Scripts’

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