Running It Twice: who does it favor?

[captZEEbo1]

Let's say two people go allin on flop, and in order to reduce variance (perhaps b/c they are playing out of their bankroll), they run it twice, meaning they deal the turn and river and whoever wins that gets 1/2 the pot, then they put those 2 cards to the side, and put out a new turn and river and the winner of the second turn/river wins the other 1/2 of the pot.

Outside of meta-game reasons (it'd be good to not let someone playing outside their comfort zone to run it twice, b/c you'd want them to fear going broke or whatever), my intuition says that this should favor someone, but I don't know for sure. Obviously if the turn and river went back into the deck and it was reshuffled, it'd be neutral ev.

I read about it here, and it sounded like it took doyle some time before he agreed to run it twice. " 'Oh, I don't know; I don't see how I could win it twice!' Doyle quickly understood that despite the fact that he had the best hand at the moment, my draw was a significant favorite to win the pot." That seems like some bad logic by Doyle, unless he was just holding out for metagame purposes.