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The only way it could be made a legit completion is to find out through the source code why the game does this, and then we can determine if it's actually legit. for all we know the game could be wrongly thinking it completed and therefor show that all objectives are complete, go on to runway, but NOT save the best time (and rightly so). Simply, the game is confused. It would be as if the hostages on frigate would escape 3 seconds after entering the boat, the run isn't legit, even if the objective is just as complete, since it happens after the run. you're just out of luck, time the ending better next time.
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Well, i respect Wouter, but I have to say he is being an ass about this whole time glitch with alex. I found that that post was mean.

He's kinda sayin "I don't care about your hard work, if the time doesn't save, screw off!" Give him the benefit of the doubt.