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Urgh... The end game clock does not count cut scenes, and only adds in your best time. Thus, if you died numerous times, or if you decide to restart a stage to get a better ranking or pick up something you missed, the game doesn't count that time.
Still, you could've looked that up.
"What's wrong? It looks like you swallowed a bug. Oh wait. You always look like that." -Jade, Tales of the Abyss. PSN ID: Amarix