When I export an animated skinned mesh from Maya using the Three.js exporter, it always appears to have a duplicate mesh combined with it that is not animated.
I've tried all the export settings I can think of and also made sure there is not another mesh being exported with it. I can reproduce the problem by skinning, animating, and exporting any mesh.
I compared my exported .js file and I can't see any difference between that file and this working three.js example:
intermediate object
with the skinned object. – davidlatwe