In the graphics settings within wow, you can set wow to have a max FPS foreground, and max FPS Background. Now if wow's settings are on, it may be conflicting with what Keyclone is wanting to do, but if you cannot change the settings for background fps then you may want to dissable keyclones option then go with wow's control over fps instead. set it to medium high on the forground, then lowish on background. That way whatever window is in the main view, will always have better fps since thats the one that matters.

I don't know how keyclone works with wow, but you may have to run wow standalone and set this, close it, then run it from keyclone. that way it will have the settings scripted already, then you dont' have to mess with it after. again I have no idea how keyclone operates with wow, so someone who's used it, or Rob should be able to explain better.