Normally, if you envelop a mesh with a chain, what gets exported is from the point of view of the bone, what influence it has on the vertex, so you have to add for all the deformers the relative weight.
Now, if you did that already and some vertices have no weights at all, then possibly you added some vertices after you have enveloped the object.
try this and you will have the situation. You should reset the pose, remove the envelope and then re-apply the envelope. Better yet, applied the envelope after you have done polygon modeling.
CreatePrim "Sphere", "MeshSurface"
Create2DSkeleton -1.65419481185095, 4.80079062646199, -0.480079062646201, 4.4505717556942, 5.87851913444406E-02, -5.87851913444482E-03, -5.71059313749964, 0, 0, 4
AppendBone "eff", -1.41788126730081, -5.4278326674693, 0.542783266746923
DeselectAll
SelectObj "sphere", , True
ApplyFlexEnv "sphere;root,bone,bone1,eff", False
DeselectAll
SelectObj "sphere", , True
SplitEdge "sphere.edge[14]", 51.7827931176601, False, False, siPersistentOperation
SplitEdge "sphere.edge[12]", 49.5000777140515, False, False, siPersistentOperation
SplitEdge "sphere.edge[106]", 38.6945341313472, False, False, siPersistentOperation
SplitEdge "sphere.edge[17]", 52.0851127006827, False, False, siPersistentOperation
SplitEdge "sphere.edge[15]", 33.4784423627871, False, False, siPersistentOperation
SplitEdge "sphere.edge[108]", 40.5742593065164, False, False, siPersistentOperation
DeselectAll
ExportDotXSI
Now if you do this, then it will be ok
RemoveFlexEnv "sphere"
ApplyFlexEnv "sphere;root,bone,bone1,eff", False
ExportDotXSI
I hope this helps.