I usually use Barkeepers friend, a white scouring pad and a lot of elbow grease for any stainless blemish... if it doesn't come off, then it's either not SS or not very good SS. I'm not sure about others, but I'm not able to imagine what a stain on SS caused by Star San would look like.. Could you post a pic?
StarSan is acidic. Phosphoric acid I think. If you left it on there to dry, then you might have some marks etched in that aren't going to be easily removed. Just consider what doesn't easily come out as giving it "character".