Mr Gibbs is in the start on the ship with elizabeth and her father but suddenly he is in tortuga (sp?) and he knows jack. when elizabeth is rescued and she gets on the ship with will she sees mr gibbs and she is shocked he is there but nothing more is said about it??
It's possible that Gibbs left the English navy, but that's speculation. There is a distinct prequel feeling to Pirates of the Caribbean and we are left to guess at the loose ends. Unless they make prequels, we will never know the deffinite answer.
Unless, of course, they reveal the answer in the sequels