Same error found (with new info)
Hi.
I have had the same problem, a fresh install of Clonekeys worked with movement but as soon as an actionbar key was hit, Clonekeys stopped working. After reading the post about window focus I did a test and got this [stage6]http://www.stage6.com/user/xcaine04/video/2161820/Clonekey-focus-error[/stage6].
The hint is actionbar. So I turned off all mods and started with a fresh Clonekeys install and all works well so far.
I will be back to what mod, probably Bongos2 the actionpanel mod, when I find it out.