I think the FFXIV client has a number of issues with timing such as this one. Things like cool down and the stamina bar very often fall out of sync. I'm guessing that it partially has to do with the client being unable to handle fluctuating frame rates gracefully. It also seems that the client fails to receive data from the server at times. Both situations lead to desynchronization of your character's various timers. Usually it isn't too bad a problem, but sometimes things get really out of sync and it can be confusing in the heat of battle.