Isn't this a question of hubris? The title claims that "Rational People Do Worse", but wouldn't a rational person surmise that there is some information/mechanism they don't have access to that the computer does in order to achieve the success rate claimed? In that case the rational choice would be to claim the single box.
The other factor not addressed is the $1k vs $1m. The calculus changes a lot based on these amounts. If it was 10 bucks vs the chance to win millions? that's the lottery. if it were $10k it be a lot harder to walk away from that.
As a thought experiment, its a lot easier to say what you think the answer should be, actually making that choice when there is real money is psychologically different.
And still.