Also one more question.
Does the weight actually change directly after you run the export skin command? Or does it change when you import the data later?
When you still had ngSkin data on the mesh, did you ever do any Maya skinning commands, like normalize or pruning or any Maya weight painting? If so, the weights can become out-of-sync. And then the next time the weights are edited or updated, they can pop into a new position.
To test that theory, you could follow all your same steps, but before you export skin, you could try flooding smooth of 0.0, so it has zero effect, but it updates the weights. And you might see it pop in the same way. Although… if that were true, you probably should have seen it happen when you normalized. So this is not likely.
(I’m not ruling out a bug with the mGear skin tool. I’ll check that. I just want to rule out any other potential bugs too.)