This happens right as I try to snap the duplicated rig to the original. (0:52). I am doing the snapping in side view, just orbited to 3/4 to give a better angle of the problem. I've tried having other bones as the active element, but the same thing seems to be happening.
Hi John.
It's hard to tell exactly but let me hazard a guess.
It's possible that each bone joint is snapping to the geometry of the treasure chest. Or that the stretch-to constraint is wreaking havoc on your def bone.
Or that one of the joints was not selected when snapping (probably the head of the def out bone). This would mean that the def bone actually has to connect in a way that isn't actually possible for it to.
You could manually try to snap things where they are meant to be. But it might be easier to just delete these warped bones and try again.
Here's a crude drawing that hopefully explains the bones that are out of place.
I had a similar issue, and fixed it by unchecking "Align rotation with target" in the Snap To settings.