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The kraken attacks do seem to be a poorly thought-out portion of the script.
Initially it is said that the kraken will persue whoever has the black mark, which Bootstrap Bill then puts on Jack. So the kraken goes off and attacks the ship where his has ended up and apparently without a specific plunger call to arms. When Jack offers the 100 souls, Davy Jones's removes the mark for the three days he is given. The second attack happens
during this period so it is fine to assume that the kraken wasn't in persuit of Jack and available for a specific call to arms. Then when Jack is about to kill Elizabeth the time runs out and the mark returns. No kraken attack between then arrival at the island with the chest. When they get back to the Black Pearl and set sail they are apparently in deep enough waters for the kraken to attack but it does not do so until the plunger of doom and then it attacks immediately so it was in the area.
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