The problem occurred for me when using the 0.01 metric unit scale in Blender (as required by the script), then scaling up the mesh in the Blender export again (by 100).
[edit] To fix it, I have to use a scaling of 1,1,1 for the ISMs. In the MS_VertexAnimationTools_MorphTargets function in the material I multiplied the WPO output by 100 to offset the 0.01 scaling. There has to be a cleaner solution tho.