i believe it has something to do with the "Location" in the cooldown part of the Cost: Cost+ field. not sure as i haven't really played with that too much but i believe changing the location from 'ability' to 'player' might do what you're after.
@rikky333: Go Give your ability's cooldown a unique link and set the cooldown location to ability. Setting it to unit makes it specific to a unit, setting to ability makes it work for all units that use this ability for that same player. Setting it to Player makes it set the cooldown for all abilities for that player I think and setting to Global sets the cooldown for everything in the game.
So the Cooldown Link field is extremely important, don't leave it empty or use the same link for different abilties unless you want them to work as one.