I stopped using the 'Focus Follows Mouse' feature
I always had problems with that feature of Keyclone as well. Interestingly, I have no problems whatsoever if I just enable xmouse (window follows mouse, whatever it's currently called in Windows), so I've done that instead!

I downloaded a little toy that lets your turn it on or off on the fly, but Google knows lots of ways to enable it in various versions of Windows if you wanted to give that a shot.

Personally, I've never looked back