After getting a comment from the creator of kanata (an awesome piece of software by the way) that he found my story amusing, I figured that I'd also post it here, partly as fun, partly as a cautionary tale. Also, I'd appreciate any tips as to what to check for in my system, it's a weird feeling to know that some stuff might have been messed up under the hood.
They moved Ctrl-Alt-Backspace behind a config iirc - too easy to hit by accident.