I think this is due to cast animation.
I have seen the same behaviour with templer shards. there is a roughly 2sek cooldown at the beginning and then the "real" cooldown starts as soon as it hits the ground.
At least in case of shards it is not a bug. For example Fancy Action Bar does kinda the same thing. The countdown start when the shard hits the ground. Only difference is, it does not display the 2 sec cooldown.
I havent played any sorc recently, but I guss it is the same thing for lightning flood.
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