it's not just a fan theory, it's canon.
if you read Pirates of the Caribbean: The Price of Freedom by A.C. Crispin, it's all about how Jack used to work for the EITC and his history with the Black Pearl, along with some really exciting adventures ^_^
it's actually a really good book, not at all what i expected, and the intended audience is for adults
they probably were trying to cut the movie shorter, and i guess it was one of their "disposable" scenes, since the back story has less effect on the main plot than the other stuff.