Sorry, Erika had not got to further investigating your issue on Friday. She often needs some personal time on the weekends
all work and no play leads to an angry Erika, then we all have to tiptoe around her for days lest she beats us again.
When you bind your mesh to bones, any change to the bone transforms (translation, rotation, scale, or shear) will deform your mesh. If you bind your mesh to bones, then apply an IK constraint and the IK rotates the bones, then your mesh is deformed. Could it be that occurred, so your mesh is deformed, then you when manipulate vertices it doesn't give the result you want? If so, you could setup IK before binding the mesh.
Or, you could position the IK target bone at the exact tip of the IK child bone so that when the IK constraint is created the bones do not rotate. To do that, before creating the IK constraint:
1) set the IK child bone to be the parent of the IK target bone,
2) set the local translation of the target bone to x, 0 where x is the length of the child bone (this places it exactly at the tip of the child bone),
3) parent the target bone elsewhere, where you actually want it (the world position will stay the same),
4) create the IK constraint.
