The Torkham border crossing between Pakistan and Afghanistan is open once again, with trucks busily ferrying supplies to NATO troops. But the 10-day closure has exposed fault lines in the relationship between Pakistan and its NATO allies that will not be smoothed over by apologies and diplomatic exchanges.

Pakistan shut down the vital Torkham supply route after a NATO air strike on Pakistan’s territory left three military personnel dead and several others wounded. While Pakistan has condoned drone strikes against insurgents inside the country, it has repeatedly said it will not tolerate active military operations by foreign soldiers on its soil.

The U.S. Ambassador to Pakistan, Anne Patterson, issued an apology for the strike, calling it a “terrible accident.” General David Petraeus, commander of U.S. and NATO forces in Afghanistan also expressed regret for the loss of life.

Eventually Pakistan relented, but not before close to 150 NATO trucks had been torched inside Pakistan.

The relationship between Pakistan and NATO, particularly the United States, has frequently been rocky, but this has been the worst dispute since NATO military operations began in Afghanistan nine years ago.

After the fall of the Taliban regime in the wake of a U.S.-led attack in October, 2001, Pakistan became a strategic partner in the region.

Since the September 11 attacks that precipitated the War on Terror, the United States has given Pakistan more than $18 billion in civilian and military assistance, making it one of the top five recipients of U.S. largesse in the world.

But the flow of cash seems to have done little to improve relations: a recent poll by the Pew Research Center showed that more than half of Pakistanis regard the United States as an enemy, rather than a friend. For its part, the United States has become increasingly suspicious of Pakistan’s professed efforts to curb the Taliban.

As more and more evidence has emerged that Pakistan is actively supporting Afghanistan’s Taliban, while battling insurgents on its own soil, people are asking why the United States has been so indulgent towards its fractious partner.

Pakistan’s main security preoccupation has little to do with the global war on terror. It is focused on India as the main danger to its stability, and according to numerous sources it has been actively involved with the Afghan Taliban as a hedge against what it sees as a pro-Indian government in Kabul. As long as Afghanistan remains mired in conflict, it cannot provide a strong base of Indian operations against Pakistan, the reasoning goes.

“Pakistan has received billions of dollars from the United States to tackle terrorism but it did nothing,” said General Abdul Hadi Khalid, Afghanistan’s former Deputy Minister for Internal Affairs. “Not only have Taliban and al Qaeda not been vanquished, they have re-emerged.”

The United States has now realized that Pakistan spent the money in assisting the Taliban, added Khalid. But rather than punish Pakistan, the United States lets them get away with it because of certain long-term interests in the region.

Ahmad Saeedi, a political analyst who worked as an Afghan diplomat in Pakistan, agrees.

“The United States is pursuing its on interests rather than forging friendships with regional partners,” he said. “The United States is following an economic-based policy with Pakistan. But now that the international community has realized that Pakistan is engaged in a double-faced policy, it has lost patience.”

Some question how much the United States can do against Pakistan, whose cooperation it desperately needs if it is to keep on with its military operations in Afghanistan. Pakistan provides a badly needed supply base for the 150,000 NATO troops stationed in Afghanistan, and, as the Torkham closure shows, it can cut off this lifeline at any time.

According to numerous sources, including Bob Woodward’s recent book on the internal White House debate over Afghanistan, the United States is only too aware of Pakistan’s ability to cause problems. With 180 million people and a healthy nuclear arsenal, Pakistan can become a dangerous focus for regional instability. The possibility of 100 nuclear warheads falling into the hands of Islamic extremists is a threat that keeps U.S. dollars flowing in a bid to prop up a weak and ineffective Pakistani government.

But Pakistan and the United States have different, and at times conflicting, interests in Afghanistan. While the main focus of the United States is on the Afghan Taliban, Pakistan is providing sanctuary and in many cases active support to those who are fighting U.S. and NATO troops.

There is too much evidence to ignore that Pakistan’s Inter-Services Intelligence (ISI) is in constant and cooperative contact with the Afghan Taliban.

In addition, Pakistan’s almost non-existent border with Afghanistan gives insurgents a safe haven in Pakistan from which to plan and conduct operations against NATO troops.

The United States is reluctant to discontinue support, perhaps because of the above-mentioned fears that the Pakistani government could fall prey to insurgents on its own territory. But inside Afghanistan, analysts see a more self-serving motive for the closeness between the two countries.

“The United States does not want to lose Pakistan as a long-term strategic partner in the region,” said Noorulhaq Ulumi, a retired general and a Member of the Afghan Parliament. “The money that the United States has invested will be lost and its interests will be endangered if it makes Pakistan unhappy. But in my opinion, even if the United States gives Pakistan bags of dollars it will continue supporting terrorism and insurgency.”

Time is running out, cautioned Ulumi. As President Barack Obama has pointed out, the cancer is in Pakistan.

“The United States should take this opportunity to rid itself and the entire world of this malignant cancer,” he said. “Otherwise, it will not be able to do anything against Pakistan in the future.”

Hamidullah Habibi contributed to this report