Jeb Koogler puts his finger on a real worry:
Musharraf's government has gone farther than just to turn a blind eye to the actions of militant groups; indeed, Grare believes that the Pakistani military has deliberately not taken down key Taliban leaders. According to one analyst quoted in the [Carnegie] report, "the current [military] operation is only directed against Taliban foot soldiers of local origin, led by insignificant leaders, whereas places like Shawal [where key Taliban leaders operate]…remain calm and quiet."
The full Carnegie report on Pakistan is here.