I think it has something to do with the polyToSubd operation that you did on the mesh. The smooth skinning is being applied to both the poly object and the resulting subd object, and that yields the double transform. If you select the mesh and look at the channel box, you'll see 2 shape items: polyToSubd... and Turtle2_polyToSubd... (names are too long type out, and I'm lazy). Somehow, you have 2 shape nodes on there, and I'm not sure how you did that. You migh have converted the poly to subd incorrectly or .... something.
There are a couple of solutions. One is to simply "turn off" the influence of one of the skin clusters. Select the root joint, select skinCluster1 in the channel box, and set the envelope to 0. That basically disables any influence that node has on anything.
The other option, which is much cleaner, is collapsing the subd hierarchy. You can do that by going to Subdiv Surfaces > Collapse History. That will create a new subd object without the low-res poly cage, but it will be a clean object and should skin correctly.