Not sure if its just my blender version or something but ya. The controller does not squash, stretch or bend the cube...
Not sure if its worth a look. Maybe I could fix it after I learn somethings about rigging ;)
the answer has been given earlier by several other people, but as this is the top question now, i will answer it again (since it is rather signficant).
you need to go to File > User Preferences > File > Auto Run Python Scripts:
hope that helps,
if you want to understand the whole rig better, Maria Luisa Carrion D. has written a detailed explanation under the title of 'Not a question. Explanation of how the cube rig works'.
julian