I'm not sure what you did, but if you went about the editing in Nifskope... it's always better to do that sort of mesh work in Blender. Nifskope is fine for simple things and finishing touches, but Blender is much better for any kind of in-depth editing (especially when skeletons/rigging is involved).
When you edit those kinds of meshes you need to export with a 'clean' skeleton, and that's something you just can't do in Nifskope.