Actually I have heard (on IMDB) that the mark Jack left on Beckett was that way back when Jack worked for Beckett and Beckett sent him to Africa to get some cargo for him... well, Jackie didn't know what the cargo was and it turned out to be slaves. And you know what? Jack let them all go free.

dear ol' Jack. Anyway, that made Beckett VERY mad and it probably cost him a lot of money so that's when he branded Jack and sank the Black Pearl (and that's why Jack has to make his deal with Davy Jones to get it back).
So mostly it sounds like the mark Jack left on Becky was just a loss of money and maybe pride...... and Jack didn't follow Beckett's orders without question (and we all know how Beckett likes his people to follow orders and do what he wants

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