It’s fascinating… just like the other problems i reported, the last patch did not fix things, but just made it “more weird” and worse.
The above mentioned method of stoping the tobii software does not work any more. It seems like now, when things fail at reboot, the very only way to fix things is to really reboot the computer. Bonus points: when this problem happens, my X-56 joystick also constantly now gets disconnected and reconnected. Whatever your software is doing with the USB, please make it stop doing that!