When joining the rover on the right to the craft on the left with an articulating arm, all the moving parts on the joining arm stopped working. All the other moving parts continued to work. I was able to reproduce in orbit with a model of the canadarm2. Again, all the parts between the root and the larger target vessel became immobile. In each case I was focused on the articulated craft during docking. I'd guess it has something to do with changing the root and therefore the direction of the branches in the vessel tree, but that's only a guess.
(Reloading the vessel from a save seems to fix the issue.)
(Reloading the vessel from a save seems to fix the issue.)