Grouped Bones not animating?

Ok so in an older version of unity like 4.2 my character worked fine with the generic rig set up. Now in version 4.5 it does not. It took me a while to figure out what was going on and i found out the new version of unity doesn't liked bones to be grouped. I used to set up my rigs like this in maya
MaleBoxer (main character group)
Joints group
hips (root joint) all other joints under this one
ctrls group
all other...

Grouped Bones not animating?