CHICAGO: In an unmistakable snub, President Barack Obama left Pakistan off a list of nations he thanked Monday for help getting war supplies into Afghanistan.    

The omission speaks to the prolonged slump in US relations with Pakistan that clouded a Nato summit where nations were eyeing the exits in Afghanistan.

Obama readily acknowledged that the tensions raise questions about whether Pakistan will help or hurt the goal of a stable Afghanistan.

Continued mistrust between the United States and Pakistan also threaten cooperation to eliminate al Qaeda sanctuaries and could undermine US confidence in the security of Pakistan’s growing nuclear arsenal.

“We need to work through some of the tensions that have inevitably arisen after 10 years of our military presence in that region,” Obama said later. “I don’t want to paper over real challenges there.”

Pakistan is not a Nato member but was invited to the summit Sunday and Monday because of its influence in next-door Afghanistan and its role until last year as the major supply route to landlocked Nato forces there.

Pakistan closed those routes after a US attack on the Pakistani side of the border killed 24 Pakistani soldiers in November.

The last-minute invitation from Nato to join the Chicago talks was a sign of hope that the rift had healed.

But it hasn’t. And Obama’s dealings with Pakistani President Asif Ali Zardari made that clear on Monday.

Zardari came to Obama’s home town expecting a separate meeting with the US leader like the one accorded to Afghan President Hamid Karzai. But without a final deal to reopen the supply lines, no such meeting was to occur.

Obama, along with Karzai, did speak briefly with Zardari on the sidelines of a large group meeting Monday. Karzai dismissed the encounter in an interview with CNN as a “three-way photograph taking ... just a photo opportunity.”

That was after Zardari had to sit by as Obama opened Monday’s session with public thanks only to the nations north of Afghanistan who allowed expanded supply shipments to transit their territory to compensate for the closed Pakistani border gates.

“I want to welcome the presence of President Karzai, as well as officials from central Asia and Russia , nations that have an important perspective and that continue to provide critical transit for Isaf supplies,” Obama said, referring to the International Security Assistance Force that is fighting the war.

Pakistani officials played down the snub.

“The supply route on Pakistan’s side has been suspended for the last six months,” Zardari’s spokesman Farhatullah Babar told reporters.

“There was really no expectation from our side that the US president would appreciate and admire the suspension of the Nato supply lines.”

The border crossing dispute is stuck over how much the US will pay Pakistan to allow trucks to transit its territory. Before the airstrike, the US paid about $250 per truck. Now, two US officials said, Pakistan wants $5,000 a truck and an apology for the deaths in the airstrike.

The Obama administration has said it was willing to pay as much as $500 per vehicle and has expressed condolences and regret, but no apology. The officials spoke on condition of anonymity because the negotiations were being conducted in private.

The prospects for reaching a deal were unclear, even as the stakes grow larger.

Babar said the government had asked negotiators to expedite an agreement, but that “no timeline can be given.”

Obama told reporters at the close of the summit that he knew beforehand that there would be no deal on the supply routes now.

“President Zardari shared with me his belief that these issues can get worked through,” Obama said. “We’re actually making diligent progress on it.”

Zardari also met with Secretary of State Hillary Rodham Clinton on Sunday and made a beeline across a meeting hall to grasp her hand again on Monday morning. The State Department said Clinton and Zardari “discussed the importance of reopening the Nato supply lines,” and of cooperating to fight terrorist threats.

The US and Pakistan have a history of troubled relations that started well before the terrorist attacks of Sept 11, 2001.

The road has grown only rockier since then. Pakistan has received billions of dollars in aid from the US over the past decade, but anti-Americanism is widespread in the country. And after years of sometimes meaningful cooperation in hunting down al Qaeda figures, Pakistan is still seen by many US officials as double-dealing and unreliable.

The transit route issue was a distraction and an embarrassment for the United States at the summit, and Obama’s cool arm’s length treatment of Zardari made it look even worse for the Pakistani president.

“Pakistan has to be part of the solution in Afghanistan, and it is in our national interests to see a Pakistan that is democratic, that is prosperous and that is stable,” Obama said.

The quarrel over supply routes is intertwined with several other disputes, including Pakistan’s opposition to US drone strikes against terrorist targets inside its borders.

In addition to closing the border crossings in response to the November attack, Pakistan ordered the US to vacate Shamsi air base, which the US was using to launch drone strikes at al Qaeda and Taliban militants.

The top allied commander in Afghanistan, US Marine Gen  John Allen, has tried to cast the supply route problem in the best possible light, while acknowledging that he’d like to see the border crossings reopened as soon as possible.

Allen said Sunday that by some measure, war stocks are higher now than when the crossings were closed.

That is thanks to an increased, and much more costly, use of alternative routes, including a network of northern routes that connect Baltic and Caspian Sea ports with Afghanistan through Russia and Central Asia and the Caucasus.