I was rigging a MakeHuman mesh with Rigify when I ran into an insurmountable skinning problem. I created the meta rig, generated the rig, but the deform bones were not placed properly so when I tried to skin the character mesh, most of it disappeared. I started again with nothing but a rigify rig, and here is what happens:
As you can see, all the deform bones are where they are supposed to be, in EDIT mode. But when I switch to Object mode (which I would have to do to parent a mesh to this armature, most of the bones dissapear.
This is the rig in object mode (looks much the same in pose mode.) I have all the layers turned off except for the deform bones, but the rest of the layers look like they are supposed to look: bone shapes, mostly. At any rate, I am running Blender 2.68a and it has Rigify addon version 0.4
How can I fix this?