To reproduce:
1) Open the attached project and open 'JointTest' scene
2) Run the scene, you will see that script disables and then enables right game object.
3) After that Animator is disabled and Ragdolls are enabled.
4) You will notice that left game object turns into default 'T' form and falls, which is expected, and right one just stays in the same position (does not turn into 'T' form) which is undesired effect.

Note: It works fine if you disable object in editor and then enable it with script while game is running. It seems that disabling object in game causes the issue.