I got the impression that Jack had gone through a lot between being brought back to life by Rose at the end of Series One, and becoming head of Torchwood. Hence why he was so much darker. He didn't return straight to present day earth, so he could have been through many experiences, several involving the Doctor past, present and even future incarnations.
One reason Jack would be excited about seeing The Doctor again would be that he too was in the situation of out-living those he loved, as well as having an exciting Space/Time-ship that could take him on some decent adventures away from the idiots at Torchwood.