I really hope it is the lighting. I can definitely see a difference between the two, but it could be chalked up to lighting and paint app. The proto looks very Indy to me. Mischevious smile. The production shots look like the same sculpt, but it looks much more serious. I prefer the proto pic.
Edit: Actually the more I look at it, the more I am convinced it is differences in paint apps. Especially the eyebrows. On the Proto, they are more rounded, which give him a more playful, relaxed look. The production piece has straighter eyebrows which give a more severe, concentration like look.