Unexpected, yes; problems, no. I'm currently re-implementing the entire thing in Clojure, as it gives me a really elegant, simple, "simulate my opponent" function (which is exciting!) and makes everything else much neater to boot. I've also gotten a friend interested in this project; he's probably going to help me build a semi-permanent results / interaction page for the project - something like this and this put together. On that second page, about shuffle algorithms, you can enter your own custom shuffling method. We are excited about having something like that for bots - visualise the data, and enter your own custom strategy to see how it performs. This lets us have a sort of long-running 'informal' tournament. But it is still on its way!
Less Wrong had a Prisoner's Dilemma contest some time back, whose results I've forgotten. Perhaps it should be rerun with William H. Press & Freeman Dyson's proposed extortionate strategies.
I hope Pinker gives a response at Edge.org, since P.D played a significant role his book "The Better Angels of Our Nature" as a source of morality embedded in the nature of logic/reality.
Hat-tip to Marginal Revolution.