Perhaps we could get the awesome programmer of keyclone to work in a key-up command some short delay after they are sent as key-downs. Any time you have slight lag or windows decides it's the focus and not WoW you will run into this problem. You can easily duplicate it by holding down your modifier and pressing your key to stop broadcasting, to simulate the loss of focus, while not brodcasting release the modifier and resume broadcasting you will now have the "modifier stuck" scenario. To remedy this situation simply press the stuck modifier for about a second and release. if you want to make a macro for showing when a modifier is stuck try this

#showtooltip [mod:ctrl] Fireball; [mod:alt] Arcane Missiles; [mod:shift] Frostbolt; [nomod] Polymorph

this macro will show a different spell tooltip dependant upon modifiers being pressed you can quickly train yourself to know which spell equals which modifier. The nice part about this it doesn't take up a key that can be keybound somewhere else.