You're right and I was unbelievably stupid. (And I even was aware of the setup you mentioned, but failed to connect it to FF!) Added an update to the post. Thanks! Please do more of this.
If its any consolation, I've found that the nasty games actually don't have Nash Equilibria if you view algorithms as strategies, so FF is as good as it gets.
In Freaky Fairness the author discusses the problem of multi-player game theory problems where all players have access to each-other's source code. He gives an algorithm called Freaky Fairness, and makes the claim that 'all players run Freaky Fairness' is both a Strong Nash Equilibrium and a Pareto Optimum. Unfortunately, as far as I can tell, this claim is false.
For reference, the algorithm of Freaky Fairness works as follows:
Calculate the security values in mixed strategies for all subsets of players.
Divide all other players into two groups: those whose source code is an exact copy of Freaky Fairness (friends), and everyone else (enemies).
If there are no enemies: build a Shapley value from the computed security values of coalitions; play my part in the outcome that yields the highest total sum in the game; give up some of the result to others so that the resulting allocation agrees with the Shapley value.
Now consider the following simple game for three players:
Conventional competitive game theory notes that each player has a dominant strategy of nominating themselves, and so nobody gets anything. Since the game potentially offers an $300 prize there is room for improvement here. Lets see how Freaky Fairness does:
If any one player deviates then the other two will split the money between themselves to ensure that this one player gets nothing, so far so good. Unfortunately if two players deviate they is nothing the remaining Freaky Fairness player can do to ensure they don't each walk away with $150, which is more than they get by sticking to Freaky Fairness.
Why does the proof given in the original article fail here? The proof assumes that the Shapley method gives every coalition at least their security value, which unfortunately it doesn't manage in this case. This is not a problem that can be fixed by a better method of sharing, as it should be fairly obvious that there is no way to share a quantity of money between three people such that any two of them get all of it.
Freaky Fairness is still a very impressive algorithm. If we define a class of 'nice games' as games where there exists a way of sharing out the winnings such that every coalition receives at least its security value, then Freaky Fairness works on all these games so long as Shapley does (where Shapley fails you can easily modify FF to find a real solution). We now just need to consider the class of 'nasty games', such as the one above. (For those more familiar with co-operative game theory, nice games are those which have a non-empty core, nasty games are those which do not).
Note: I was quite surprised that none of the smart people in the comments section of the original article noticed this, which leads me to think it's quite possibly wrong. Any criticism is welcome.