The sticky key thing comes from the fact that a new window (the task manager in your case) gains focus and stops the sending of keys in keyclone. The result is alt and ctrl are sent as being pressed down but before the "key up" can be sent keyclone stops sending keys. This is done by keyclone to prevent sending keys while you are typing in something other than the game. An easy way to fix it is go back into the game and simply press ctrl and alt then release them. Once the key up is sent to the alts all will work as it should. It happens to me a lot when alt-tabbing to another window, I have learned to either stop broadcasting prior to tabbing out of the game or hit alt again when I tab back in.

As far as the CPU hogging instance bug...I get that from time to time as well and haven't a clue as to what causes it. It never occurs when i run one instance, and it doesn't seem to be tied to keyclone, as it manifests itself while using other kb broadcasting software. I found that minimizing the instance and restoring it often fixes the problem.