It seemed to me that the armature is simply not activated even when using run armature actuator. Adding a simple dummy action to the armature and playing that for a moment solved it for me as a work-around. After that all bone constraints also kicked into action.
I did not check spawning multiple copies before but now I do and it is indeed quite anoying. Each armature is flipping over all different ragdolls + rest pose.
As far as I can check the constraint targets in python are OK, (same group as armature object). So the bug must be somewhere deeper into the system …
The only way it did work for multiple copies was to save the original file multiple times, each time linking to a different source file. Which is kind of beating the idea of linking files to a single source.
There is a bug in the constraints connected to a static object and if you offset it from the world enter. Actually I don’t have a fix for that. The only thing you can do is to use 6DOF constraint or set the static object to rigid, dynamic or sensor.
There is also a bug in the run armature actuator. It does not work correctly with dubli groups. You can start the armature if you run an action just with one frame.