Pakistan shut a key border crossing because of a Nato air-strike which killed at least two Pakistani soldiers.
The US has now apologised for the attack and Nato says it expects the border row to be resolved soon.
But relations with Islamabad have been placed in further doubt by a White House report that has questioned Pakistan's willingness to curb militants.
The leaked report says Pakistani forces are avoiding "direct conflict" with the Afghan Taliban and al-Qaeda.
Is the US strategy in Afghanistan still on track? Is Pakistan obliged to shoulder a burden too heavy, or is it dragging its feet in the "war on terror"?
Joining the programme are Mosharraf Zaidi, an independent Pakistan analyst, Mullah Abdul Salam Zaeef, the former Taliban ambassador to Pakistan, and Simon Henderson, a senior fellow at the Washington Institute for Near East Policy.
This episode of Inside Story aired from Thursday, October 7, 2010.