I too am doubting software and favouring a much more mechanical or electrical type problem.
When the fault manifests itself, the gear leaver feels locked rigid. This makes sense as the gearbox is under load. When the quick shifter is working, there is just a title bit of resistance and the lever just snicks up or down. For some reason or another, the system is not killing the ignition for the fraction of a second it takes to take the load off the gearbox. I don’t think it’s mechanical, as the normal (third world) clutch method works fine and I can change up the box by closing the throttle (unloading the gearbox and drive) and flicking the gear lever up. That smells to me like some sort of electrical / electromechanical problem, within the short shifter itself or between the shifter and the gearbox.
Mechanically, the external linkage is sound. That is for sure. I have had a good look at it now I am back at home.
What I can’t understand is why, after shutting the bike down on the Chunnel, it worked once and then not again, all the way back to London. It is almost as if something switches off or becomes out of line. Anyway, BMW original manufacturer’s warranty can sort it out. That’s what I ‘bought’ when I bought the new bike.