Not sure if this is a bug or intentional, I noticed the same thing. When I switch windows, my mouse focus stays with the old (dead toon) window.

I was wondering if this was because I don't play with "focus follows mouse" and maybe keyclone does so he didn't notice this behaviour?

Basically, I was hoping it could be made to automatically switch mouse focus when I use this so I could just keep on truckin' in the new window without having to grab the mouse and click in it.