after dinking around with starting them up in different order, with/without keyclone, logging in one by one or logging them all in at the same time It still didn't make a difference.

I did find out that it will only send keypresses to the main window and the most recent window, ie
If WoW-A is up and I tabbed to it from WoW-D, It will only send key presses to WoW-D and WoW-A but not to the other two