I managed to fix it. It was a strange anomaly I could not reproduce yet.
It happened that "Shutdown" was part of a three-command sequence I made months (years?) ago. It was the last command of the sequence with the first one disabled. Restart of StrokeIt or reboot did not help. Then I replaced "Shutdown" with "Temporarily Disable" which did not work either, so I thought they have bugs.
But after re-enabling the first command it suddenly worked again and now it works with re-disabled first command, too. I cannot make it out-of-order again so it might have to do something with my config file, probably saved by some earlier version of StrokeIt. It's strange, though. I thought StrokeIt saves config files every time it shuts down. I don't remember messing with that part of the config manually. Anyway, it's gone, and it seems it won't come back.
Thanks for the quick reply and I apologize for the false alarm.