I am only guessing, but is it possible with a known spot, like tape residue which should be easy to remove, but it sounds like what you are facing could have been an attemt to remove with a more solvent based cytrus sol type product and what you are left with is a shadow of the solvent inside cause the granite is so porus??
another thought, The chem company that makes Jim M spotter for him also has one of the most water soluable citrus solutions I have tried. Swenska, Big John OlsOn carries their stuff, Mixed Rite, yeah, that what their called. Would chasing the stain and then flushing with a more water sol product help?? Just a thought..