"It was Jack's hurt and confused expression when the Doctor disables his vortex manipulator, basically telling him, through his actions, that since Jack doesn't want to go travelling with him, that he's not going to be travelling at all, got me thinking. I guess it was because the Doctor could, even after the 'year that never was' treat Jack so poorly."

Well written story and thank you for raising the question about how Jack must feel.

It was that part that got me to. He was a Time Agent before they met and could have damaged the time line before, but he never did. Sure he accidentally caused some damage in the Empty Child, but we, the viewers, were made to feel that the Doctor trusted him. I can't see why after ever great think Jack has done, the Doctor would disable it again.