I can not reproduce this problem. Can you post some screenshot or mesh?
With Blender 2.62, matrix indexing was changed to conform to standard notation.
So there is the update for GoB.
(Just replace the two files in the .zip)
On Blender side, a bonus:
Shift+click on the Blender icon to create a cavity layer for the selected mesh (it is a vertex color layer).
It is really really slow so use it only for static mesh!
You can use the 'Dirty Vertex Colors' too.
Select the vertex paint mode and select 'Dirty Vertex Colors' in the paint menu.