Washington has again learned that while it can do little to change the Pakistani army's subversive role in Afghanistan, it can do even less without it, writes Graham Usher Last week the United States and Pakistan held their third top-level meeting in Washington in a year. It seemed all sweetness and light. Barack Obama pledged $2 billion to the Pakistan military over five years. Secretary of State Hillary Clinton said the US had "no stronger partner" than Islamabad in "counterterrorism". And Pakistan Foreign Minister Mahmoud Qureshi thanked Washington for the help it gave during the floods that inundated his country this summer. Yet, behind the smiles, actual US-Pakistan relations are in crisis. The "strong partnership" masks a relationship at odds over strategies to do with war and peace in Afghanistan, the foreign policy priority of the Obama administration. We are "coming through a period of tension", said a State Department official. Tensions flared on 30 September. Two NATO helicopters entered Pakistan airspace, killing three "militants", who in fact were Pakistani soldiers. The Pakistan army responded by closing the Khyber Pass border crossing, through which NATO supplies pass to Kabul. Over the next 10 days backed-up NATO convoys were ambushed by Taliban and other militants, leaving 150 trucks burning wrecks. After profuse American apologies -- and quiet promises that there would no more NATO incursions into Pakistani airspace -- the border was reopened. Every diplomat in Kabul, Washington and Islamabad believes the Pakistan army or its military intelligence ISI agency was behind the attacks on the convoys. The Khyber skirmish confirmed two things. The first is that the US and NATO remain dependent on Pakistan for their war effort in Afghanistan. The second is the two militaries are now at issue over what America believes is the fundamental reason for the insurgency's tenacity in Afghanistan: the existence of "safe havens" in Pakistan. The US wants the Pakistani army to go after the sanctuaries, particularly those of the Haqqani network in North Waziristan and the Afghan Taliban leadership in Quetta in southeast Pakistan. The army has permitted CIA drone attacks in North Waziristan, killing scores, including Al-Qaeda fighters and anti-state Pakistan Taliban militants as well as civilians. But it has banned any attacks around Quetta. It sees both the Afghan Taliban and Haqqani network as pro-Pakistani movements that serve as a hedge against Indian influence in Afghanistan and, in the future, will defend Pakistani interests in any Afghan political settlement. Washington sees the Afghan Taliban and Haqqani network as the most lethal core of the insurgency. And it sees the existence of sanctuaries in Pakistan as rendering effete any offensive against the insurgents, such as the current "surge" in Kandahar. The Khyber clash marked the continuation of the dispute by other means. Rightly or wrongly the Pakistani army saw the NATO incursions as dress rehearsals for direct US ground operations against the havens. These would not only threaten "allies" like the Afghan Taliban. They could serve as a green light to the Indian army to mount similar incursions against militant camps on Pakistan's eastern border. This is why the army responded so fiercely, enlisting the Taliban to its side. In Washington the Pakistan army was reportedly warned either to "cooperate" with the US on the safe havens or else face cuts in aid. But the US government knows it has little real leverage. Khyber demonstrated where the real leverage lies. The same is true for any Afghan-led peace process. Recent weeks have seen a flurry of reports that the US and NATO are "facilitating" contacts between Hamid Karzai's Afghan government and "commanders" from the Afghan Taliban and Haqqani network. According to Pakistani sources, Islamabad has not been invited to the "talks", reflecting Karzai and perhaps the US desire to keep Pakistan at arm's length. If so, the contacts will go nowhere. In February the ISI scuttled another attempt at rapprochement that excluded Pakistan by arresting 23 Taliban leaders. These included senior figures crucial to any negotiations. The message was plain: either Islamabad will be part of an Afghan peace process or there won't be one. Any "intention to secure Afghanistan without Pakistan's involvement... will not work," said a Pakistan military official in Quetta. But what does Islamabad want? The charge of Karzai is that the Pakistani army still sees Afghanistan as a "fifth province", providing strategic depth for its regional rivalry with India. Analysts in Islamabad discount this. For sure, the Pakistani army does not want a pro-Indian government in Kabul. But it would accept a "neutral" one -- blessed by Afghanistan's neighbours -- that would recognise Pakistan's western border: something no Afghan regime has ever done. It also wants constructive US engagement not only in the Afghan peace process but also in a Pakistan-Indian one, dormant since Pakistan militant attacks in Mumbai in 2008. Obama is due to visit Delhi next month. According to US media reports, he will oversee several arms agreements worth billions of dollars, consolidating India as a strategic ally. The Pakistan army will be watching but also listening in case Obama says anything about the divided territory of Kashmir, cause of three Indo-Pakistan wars and roiled this summer by mass Kashmiri protests for independence. As presidential candidate, Obama said progress towards peace in Kashmir would help Pakistani "cooperation" in Afghanistan, where Indo- Pakistan proxy wars are fought between the Karzai government and Taliban insurgency. He has said nothing about Kashmir since he became president. Yet, far more than aid or incursions, what he does about India and Kashmir will influence whether Pakistan acts the spoiler or enabler in Afghanistan.