It might be that, because of opening keyclone last, keyclone doesn't yet see the windows (altho I believe it should, might be mistaken)

Just open keyclone first and in Keyclone Options at commands make two commands, one per character, and open WoW with the commands in keyclone.
(You can also set maxfps and maxfpsbk with these commands. Specifically maxfpsbk should always be used at around 15, in my opinion.)



edit: Also, make sire you run keyclone as administrator in Windows Vista. Does that automatically for me since I run vista as administrator, but just make sure'you do that. :P