Fletch, if you haven't used the phosphoric acid treatment on what you describe it is possible it will continue to rust. The situation you describe is why I used phosphoric acid in the first place. If you treat with phosphoric acid any remaining rust in those pitted areas should be converted to iron phosphate instead of iron oxide and become essentially inert. Leaving any rust behind can, and many people say it will, rust again at some point.
That is one of the great advantages to media blasting- it gets all those little rust pits cleaned out.