Its not relating to you not having removed the predefined ALT+whatever keys in wow? Just a suggestion.

You should also check if keyclone got all 5 instances of your wow registered in the "fron" of the application (the big window).

You can also check if the icon on your toons get "pressed" when you hit example the button 1. I had a similar problem, but found out it was a broken macro on one of my toons. I was going nuts!

Also, the final thing. If you have closed keyclone, make sure the program is actually closed in the task manager. Try restarting only keyclone when you have your 5 instances of wow open.

Just some suggestions....