On my MacBook Pro, I occasionally use external keyboards, generally Windows ones and things have been fine.
Yesterday, I plugged in a new one, remapped the command/option keys so the windows/alt keys were in the same configuration, again, nothing new here. However, this time when I unplugged the USB keyboard, the laptops option/command keys remained switched.
More annoying is that if I go into the System Preferences -> Keyboards -> Modifier keys, remapping the keys to actions does not work. I can use the drop downs to disable any specific keys, but switching the behaviours does nothing. (Cmd/Option obvious, tried remapping anything to caps lock and a few other combinations, no joy. Restore defaults set the configuration to what I'd expect, but the settings are evidently ignored.)
So: Any ideas?