I'm going to throw out a very generic/simplified example. If the game engine expects the animation skeletal rigging to be in a specific sequence, for example left shoulder right shoulder left hip right hip, and the model has anything in a different order, or has extra/less anchors/joints/etc, body parts are going to end up where something else is supposed to be.
so in short it doesn't fit on the new models...
Goddamnit..the dream is dead.