It's most likely the key you bound this macro to, lets say it's for example 1, is still being bound in your ingame wow keybindings as ctr-1.

So it's not that keyclone isn't passing it, but probably that WoW doesn't recognize the keybinding as the macro. Double check your keybinding lists and make sure the button you bound it to doesn't already have a ctrl-button bound somewhere else.