It does sound a simple fix, as you say, like a cookie problem. But I've had the cookies changed several times and I'm still getting the same thing. But as I said, it is a problem and I do get fed up with it but it isn't that big a problem.
It isn't the first time I've had strange things like that happen. Take my car for instance, it had an intermittent misfire when the engine was under load but when it was in 'park' or neutral it was ok.
Several $000 later a wire in the electronic ignition system was found to be at fault, the plastic coating had failed and the wire occasionally shorted out causing the misfire. That was only discovered when the ignition system was replaced and the old one tested, part by part.