The 6 second cool down will only reset AFTER 6 seconds of not clicking on the macro key. Thus, after a 3 second cast of a spell, there are still 3 seconds left to hit the macro before the reset occurs.
At least, that's my understanding of the timer reset. New to writing macros.
If you don't want to have the macro reset until you're out of combat, use "/castsequence [reset=nocombat]...". This will reset the macro everytime you leave combat.
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