I know there's a fix for this, because I used to have this problem and figured it out. If you see a blank line at the top of keyclone's main window's list, that is basically the desktop, so keyclone is passing the keys to that as well. Try selecting the blank line and hitting remove. I think the the permanent fix is to setup keyclone's commands system and use that to launch your instances of WoW.exe and then turn off "Auto add windows" in the keyclone options.