In spite of what the article claims, I think that there may not have been any major disagreements between Bush and Putin regarding terrorism or Iraq. What Putin said is true, and I believe it is consistent with U.S. policy. This may not be entirely obvious now, with the focus on Iraq, but our attention will turn elsewhere after Iraq. The war will take time, and we cannot do everything simultaneously.
Bush and Putin may even have agreed to help each other out a bit. Putin can say things about Pakistan, for instance, that Bush cannot right now.
There does appear to have been some contentiousness between the two presidents at this meeting, but I think it was primarily on the subject of NATO expansion.
I'd say that's a real good surmise since the Russians had been promised repeatedly in the past that it wouldn't happen.
We may be having some chickens come home to roost one of these days.