OK, I just checked and it seems that all 3 stones are different. The one Richard gave to MIB, the one that MIB was playing with when Jacob approached him and told him that it was nice to see that he got his present and the one that was on the scale in the cave. Although I think they are supposed to represent the same idea or concept. I did notice something else that would suggest that time has passed since Jacob gave the MIB the bottle of wine and the time that he smashed it. Take a look at the bark that the MIB smashed the bottle on before Jacob approaches and take a look at it just before he smashes it. It's like it has a tar type substance on it just before the bottle gets smashed. Also the clouds in the sky are different before and after this event. Don't know what that means but take it for what it's worth. Sometimes I hate re-watching an episode or scene from Lost because I always see something else in a different light that just leads to more questions.
Everything that we know is just a theory until it is proven wrong. Take the reality that we live in, everything we know about science is theory until someone comes up with something better to take its place. So with that said why does everyone critique everyone else's theory? Just because you may not be brave enough to come up with something that explains what is going on doesn't give you the right to criticize those who have. This isn't the real world and the events that take place in this series are simply made up. The writers know what direction they will take and how they will end it. We are just along for the ride but since you came to this website and others like it I can only assume that you have ideas about what you think will happen and should be open to those ideas that aren't like yours. If we all thought alike then there would be no need for any forums at all as we would already know the answer. This is just a good mystery that we all have the pleasure of enjoying. Not everyone will be right in his or her ideas and with that I say so what. I would say don't put down someone else's idea just because you don't agree with it. If you find a fault with it that you can prove post that and leave well enough alone. Just my 2 cents.