The crux of the problem is related to possibilities of what the host will do.
If you know that the host will not turn over the winning cup, then you would switch and this is why:
If the host doesn't know where the coin is, there is a 1% chance that it is under any of the cups. If the host turns over cup after cup and finally 2 of them are left, the same original 1% probality apply to both cups that is was originally under the 2 remaining cups.
On the other hand, if the host does know where the coin is and leaves 1 cup overturned, there is a 99% probability that the cup left has the coin.
Here's why, in the case where the host doesn't know where the coin is, if you were to play the game 100 times, let's say you have perfect execution of the probability. In this case, the host overturns the coin 98 times before the end of the game and 2 times he doesn't. The 2 times he doesn't, you get to play the game. (again, I'm considering ideal situations where all possibilities are executed in order). So in the 2 games where it isn't turned over, once it's under your cup and once it's under the host's cup, so your chances of winning whether you switched or not were 1 out of 100
In the case where the host does know, all 100 times you will be left with a cup to choose from. In this game, if you played all 100 times, you would win 99 times out of 100 by switching.
This is why the host knowing where the coin is located is important, because otherwise, the possibility of the host overturning the cup with the coin disrupts the advantage that you'll get by knowing that the host knows.
yes it is confusing, I even didn't consider this in my first post until I thought about it.
Quote from sprstpd:
You've got to be kidding me, right? The coin knows the intent of the host? If there were 100 cups and the host randomly flipped over 98 of them and there was no coin underneath them (the host got very very lucky), you are telling me you wouldn't switch?