The stone he put in its place looked nearly the same as Jon's stone, but it wasn't. It was the Time Travel Stone.
It worked just like the normal stone, except that after a wish was made, both the wisher and the stone were transported to another time (either in the past or the future) before the wish was granted.
So, if Jon wished for a brand new car, then he might be transported to the year 1977, before the wish was granted, giving him a brand new 1977 car, since that car would be brand new ... in 1977.
The only wishes that wouldn't be granted were ones in which the wisher wished to be transported back to his or her own time (the present, in other words), or a specific time.
So, if Jon specifically wished to travel back in time to the Middle Ages, his wish wouldn't be granted. But if he made a non-time travel wish, he might be transported back to the Middle Ages, as part of the side-effect of the stone. But he also had just as much of a chance of being thrown 5,000 years into the future. It was all just random.
