I would mention it to your girlfriend. Just say, "Hey, sometimes your sister makes me feel a little uncomfortable. I don't want to be rude to her, so do you think this is just kind of how your sister acts? Or do you think she is coming on to me?"
Some people are what we call S*&T stirrers. And, all they want to do is cause problems. You just have to be the best person you can be until they realize there is nothing to stir.