After saving, and then reloading, all of my custom bone shapes are gone.
If i reload an old file, the shapes are there, but if i keep saving again, eventually they will not be there when i reload.
Does anyone know about this? Is it a bug?
Thanks 
I found the bug!
If you add an Armature actuator with an always sensor, run the game engine, and then save the file, it kills all the custom shape objects for the bones.
This is a game engine bug.
Even though I can see all the objects, after I save and reload, they’re all gone…
Edit: It seems to be fixed in Blender 2.7