I use KeyClone on my main computer for multiplexing and Octopus as my software KVM to control my 3 PCs. Ever since upgrading to 1.9g, when I go from one computer to another, my main computer switches focus to all 4 wow windows about a half second apart (you can see them selected on the taskbar.) So if I have my main window as focus, when I go to my second computer and back, focus is now on a different window. It also causes all the other windows to have the "new activity" blink on the taskbar. If I have another window on top of all my wow windows (say, firefox) then all the wow windows will be brought to the front above it.

My keyclone settings are very basic; I do not use focus follows mouse (although even with it on the same thing happened.) I start up all 4 of my wow instances manually and don't use the built in maximizer settings. No mouse-maps, no round robin, etc.