Instantiated ragdoll behaves differently than when placed in scene manually

Question: Why does my ragdoll behave differently when instantiated versus when it's placed in the world at authortime?

Details: I have a rigged ragdoll model of a dog that is stored in a prefab. I did not use the Ragdoll Wizard to set its joints as it seems like it's geared toward human ragdolls. So I added character joints manually and set the properties according to a reference I found on dog locomotion. The dog skeleton is composed of 29 rigidbodies/character joints each with a mass of 1. The root object also has a rigidbody attached and I have its mass set to 29 -- the sum of the masses. (Setting the mass of the root rigidbody to something low ironically makes the dog very heavy while setting the masses of the joints to something low causes the dog to go into freakish convulsions so it seems that these are the only settings that work as far as masses go).

The problem I have is that when I place the dog prefab manually into my object hierarchy at authortime and set him loose with gravity, his joints do bend with the proper degree of fluidity and twist/swing range that I specified. However, when I instantiate the dog using var newDog = Instantiate(ragdoll_dog, position, rotation), he falls like a rubber duck -- way too loose! What might be going on here?

Appreciate any insights. I can't seem to figure this one out.