If the meter settings are good for exposing Fuji ISO 100 film, perhaps it's the camera that's not correctly calibrated? ISO in the digital world is all relative. It's a setting to make the new cameras work with all of the other toys we have.
My S1 was dead on whatever meter setting worked for film. My S2 seems to be a 1/3 of a stop off. I've used that rule and been happy with the readings.
Bob