Been doing this 3D-modeling thing for almost 20 years and I've never come across anything like this. Why would everything work perfectly fine up until the point it's made a playable asset makes no sense. Like from where does the harness find a different armature to follow? Does the plugins you have add one?
Though, I'll mention again the previously mentioned animation Action sets the Viwi armature has in it. They have names like "Action.001", "Export Pose", "FluffyTailPose". They were actually a major headache for me when I was making the Viwi into an avatar on Resonite.
In fact, when I play a few keys forward on any of the Action poses, the armature plays into the Rest Pose. And from the look of things, that thigh strap clipping in like that for you is where it would be when in rest pose.
So, if there is a way to remove those Action poses from the armature, we might be on to something?