For the moment at least, Secretary of State John F. Kerry appears to have patched up the fraying relationship between the U.S. and Afghan governments that just two weeks ago appeared to be at the point of rupture. Flying into Kabul on a previously unannounced visit and engaging in what the New York Times describes as “nearly 24 hours of talks and meetings” with Afghan President Hamid Karzai, Kerry revived the floundering negotiations for a bilateral security agreement that will provide for a limited but long-term U.S. military presence in Afghanistan following the end of the NATO combat mission in December 2014.

The security pact, which must be reviewed by a loya jirga (an assembly of some 3,000 Afghan tribal elders) and then approved by parliament, could even now unravel over the still-unresolved issue of whether remaining U.S. troops will enjoy the airtight legal protections that Washington is insisting on. But if the agreement holds, it would represent a striking feat for Mr. Kerry, who is rapidly emerging as a more consequential figure than his predecessor.

It also promises to bring some stability to a wartime alliance that has long pulsed with mistrust and suspicion. The acrimony regularly leads Karzai, once seen as America’s hand-picked partner in Kabul, to denounce the Western military presence in Afghanistan as a foreign occupation. Three years ago, he accused the West of meddling in the country’s internal affairs and bizarrely threatened to join forces with the Taliban forces that NATO and his regime were supposedly united in opposing. That particular outburst caused the White House to warn that it was thinking of retracting Karzai’s invitation to meet Mr. Obama in Washington.

During another quarrel a year later, he gratuitously vowed to come to Islamabad’s aid in the event the U.S. attacked Pakistan. And his excoriations of Washington were so vehement earlier this year that the top U.S. commander in Afghanistan worried that they would stoke attacks on Western troops by rogue Afghan soldiers or even presage assaults on NATO installations by Afghan army units.

The accumulating animus had gotten so bad that it threatened to derail the security-pact negotiations. Two weeks ago, Karzai gave a stinging interview to the BBC, in which he charged that the U.S.-led military effort had “caused Afghanistan a lot of suffering” and suggested that NATO combat forces were welcome to leave.

For its part, the Obama administration was signaling that it would be happy to oblige. Earlier this year, it put out word that Mr. Obama may not keep any troops at all in Afghanistan after 2014. And following the BBC interview, the Washington Post reported that:

“the White House appears increasingly willing to abandon plans for a long-term, costly partnership with Afghanistan. Despite the Pentagon’s pleas for patience, much of the rest of the administration is fed up with Karzai and sees Afghanistan as a fading priority amid far more ominous threats elsewhere in the world.”

The frustration in Washington with Karzai’s antics is more than understandable. The Afghan leader habitually uses the foreign governments propping up his regime as scapegoats for his own failings. He is consistently given to playing to his domestic constituencies in ways that strike Western countries that have sacrificed lives and resources for his government’s survival as profoundly impertinent and ungrateful. A less mercurial, erratic and distrustful figure would no doubt make for a steadier ally.

Nonetheless, Karzai’s numerous faults do not diminish the Obama administration’s own sizeable responsibility for the deteriorating relationship. The New York Times threw light on these derelictions when it noted that Mr. Kerry’s “relatively warm relationship with Mr. Karzai, a rarity for any American official these days, had made the difference” in the security pact talks. They also caught the attention of the Washington Post when it commented in early 2012 that “Mr. Obama and his aides have done much to damage the relationship between the two countries” and that “is it any wonder that [Karzai] has grown increasingly resistant to the Obama administration?”

Strangely for an administration that took office trumpeting the Afghan campaign as a “war of necessity,” it conspicuously failed to put much effort into cultivating strong bonds with Karzai. The Obama national-security team had criticized the Bush administration for maintaining too cozy a relationship with the Afghan leader. President Bush held regular videoconferences with Karzai.

But the new administration went to the other extreme. Ahmed Rashid, a widely-respected journalist with good sources in Kabul, observes that the problems started with candidate Obama’s July 2008 trip to Afghanistan, when he made the amateurish mistake of meeting first with one of Karzai’s political rivals. The episode was a serious gaffe, needlessly antagonizing the deeply insecure Afghan leader and setting the tone for the administration’s strained ties with him.

The problems continued when Vice President-elect Joe Biden roughly informed Karzai that his days of easy access to the Oval Office were over. Rajiv Chandrasekaran, an associate editor at the Washington Post, quotes Biden telling the Afghan leader that “You’ll probably talk to [President Obama] or see him a couple of times a year.”

Two years later, as bilateral ructions began to pile up, Obama paid a surprise visit to Afghanistan aiming to mend fences with Karzai. Yet, having landed at Bagram air base just north of Kabul, Obama chose to return quickly to Washington rather than wait out a dust storm that had grounded the helicopter that was to take him to the presidential palace. As the New York Times reported at the time, the two wartime partners never laid “eyes on each other, even though they were just 35 miles apart.” Karzai viewed the incident as another in a growing number of deliberate snubs.

Some of the blame for these frictions can be chalked up to Mr. Obama’s widely-noted deficiencies in forging strong personal ties with other leaders, whether on Capitol Hill or in foreign chancelleries. But other administration officials also rapidly undermined their own connections with Karzai. The clumsy attempt by Richard Holbrooke, Obama’s special envoy on AfPak affairs, to line up alternative candidates in the 2009 Afghan presidential election meant that his effectiveness vis-à-vis the ever-suspicious Karzai was ruptured a few months following his appointment.The Afghan leader, even four years later, remains bitter about these machinations.

Similarly, the relationship between Karl Eikenberry, the U.S. ambassador in Kabul from 2009-2011, and Karzai was irreparably damaged in late 2009 when cables were leaked in which he castigated the Afghan leader as “not an adequate strategic partner.” Things only got worse when Eikenberry described Karzai as “a paranoid and weak individual” in communications that were disclosed by WikiLeaks a year later.

Compounding the problem yet further was Obama’s swift dismissal of General Stanley McChrystal in June 2010 for perceived insubordination. Rashid comments that the general was the only U.S. official Karzai trusted because McChrystal “showed deference to him in decision making and treated Karzai’s criticism of U.S. military tactics with respect and thoughtfulness.”

The strained communications have fed Karzai’s suspicion that the Obama administration, in its rush to end the longest war in U.S. history, is willing to go over his head and make a separate peace with Pakistan and its Taliban allies. This notion animated several events in the last few months. The first is the flap this past summer over the opening of a Taliban representative office in Doha, which was suppose to facilitate diplomatic talks on a political settlement in Afghanistan. Washington has reportedly worked closely with Pakistan on preparing the ground for talks with the Taliban but the sovereignty-minded Karzai felt he had been left out of the loop.

His sense of betrayal was quickly exacerbated when U.S. forces seized Latif Mehsud, a senior Pakistan Taliban commander, from the custody of Afghan intelligence operatives who reportedly had spent months trying to recruit him as an interlocutor for peace talks. Afghan officials told the Washington Post their engagement with Mehsud was “one of the most significant operations” undertaken by the National Directorate of Security, the country’s main spy agency.

A final episode has to do with the fate of Abdul Ghani Baradar, the Taliban’s second-in-command who has been in Pakistani custody for the past several years. Baradar is supposedly open to striking a peace deal with Kabul and in an attempt to jumpstart talks with the Taliban, Karzai has pressed Islamabad to release him. But Pakistan continues to keep him under wraps, a result that Karzai angrily attributes to U.S. interference.

The Obama administration can also be faulted for not heeding Karzai’s complaints about the strategic conduct of the Afghan war and for sending decidedly mixed signals about what it hoped to accomplish. As he hinted at in his BBC interview, Karzai has long been critical of the population-centric counterinsurgency (COIN) approach adopted by the Obama administration, believing that it resulted in needless civilian fatalities that in turn alienated the Afghan people from his government while doing little to interdict the influx of Taliban fighters from their safe havens in neighboring Pakistan. Moreover, Karzai held that troop-intensive COIN operations in the countryside disrupted important tribal dynamics in the Pashtun areas that are bastions of Taliban support. On this point, Chandrasekaran writes that “Through all of his flare-ups, Karzai ‘is sending us a message,’ a senior U.S. military official told me. ‘And that message is: I don’t believe in counterinsurgency.’”