While the U.S. can take Pakistans repeated protests over UAV attacks, against Taliban/al Qaeda targets, as a pro forma sop to nationalist sensibilities, the Americans take more seriously Pakistani claims that they will resist any American incursions on the ground. A UAV is much less of an intrusion than troops. This has led to the suggestion that if enough Afghans could be trained to handle special operations, they could probably operate in the border regions with minimal negative reaction from the Pakistanis. There are already some Afghan inel operatives working both sides of the border, to help with running the informant network. There is a growing effort to develop an Afghan SpecOps capability, which officially meant to go after domestic threats (Taliban and al Qaeda). But once there are a lot of Afghan operators, there will be a temptation to let them wander across the border.
Given Pakistans recent offensive in the Swat valley, and elsewhere, it seems likely theyre working with U.S. intel people. This is a very tricky business, given the ties ISI (Pakistani intel) has to some Islamist groups. But the United States has been working around ISI interference for decades, and the success of the Swat operation, and the hunt for terrorist leaders, appears to bear this out.