Ubuntu 13.04 64 bits
I've attached a sample blend file with 2 Armatures that belong to 2 different groups that are called as follows:
Well, the name of the group correspond to where I have added a driver in the armature. So, one armature has a driver in the armature layer properties, and the other one has it in the layer properties of one of its bones.
Now, If you link these groups into a new blend file and make a proxy of each armature, you'll notice that in the latest GIT, everything gets locked, that is, you can't move any bone in pose mode, and not even the empty of the group. I've come to the conclusion that these drivers, which were working perfectly well with linked rigs in 2.69, are the cause of the problem in GIT.