kimdonga Do you remember when the bones bound that mesh in what state? For example, whether the mesh was bound to the bones before or after the physics constraints were applied to those bones, or whether it was bound in setup mode or during animation in animate mode. If the vertices move when you adjust the weights, this means that the bones have moved since the bones were bound to the mesh. Binding the mesh at the appropriate time, i.e., when the bones are in their default pose, should prevent the vertex positions from shifting when the weights are changed.
If it is difficult to remember, simply redoing the mesh bindings may be a quicker solution.