It's a bit hocus-pocus since I never used Maya, but the double-layered approach sounds very logical to me. Dunno if there are bridges or multiple root bones, but I'll forward that question. But I can see there are some additional (control?) joints. Those don't have the "eSkeleton" type so I ignore them, although I still do traverse its child nodes.
Just tried it, and, not a complete surprise, same results. So I'm pretty sure now the problems start in Maya already.