A U.S. official confirmed the meeting and put a positive spin on the negotiations: “Panetta and Pasha had a conversation that reflected a sense of partnership and desire to move forward. This wasn’t some kind of ultimatum session, as some press reports have suggested it might be. The two leaders discussed common interests and a few concerns, all of which can be sorted out.”

The Times story said that about 335 CIA officers, agency contractors and Special Forces operatives were being asked to leave the country. That number wasn’t possible to verify in Washington. [UPDATE, April 12, 10 a.m.: That number apparently didn’t come up in the Panetta-Pasha meeting, and an ISI source in Pakistan said Tuesday that he couldn’t confirm it, either.] And in a sense, the detailed body count misses the real point: The  Pakistani military wants the CIA to stop “unilateral” operations inside its territory — meaning drone attacks as well as undercover ground operations — that don’t have specific prior clearance.

The Pakistani demand reflects tensions between the two countries that reached a crescendo with the January arrest of CIA contractor Raymond Davis after he shot two Pakistanis. That case was resolved when the U.S. agreed to pay more than $2 million in “blood money” compensation to the victims’ families. But as I wrote at the time, the larger Pakistani demand was for a change in the rules of the game so that it was treated more like other close allies, such as France, Israel or Jordan, where the CIA doesn’t generally conduct unilateral operations on the host nation’s territory.

[“Yes, we have asked CIA to come clean on and give us visibility into the operations of people like Raymond Davis of which we think there may be some 40 - 60 such operatives in the country,” the ISI source said in an e-mail Tuesday. “How many have left or are in the process of leaving is something which only the embassy can confirm.”]

If the past is any guide, the tone of private discussions between Pasha and Panetta will be less antagonistic than Pakistani press leaks to the Times’ veteran Islamabad correspondent, Jane Perlez, would indicate. ISI officials often reach more cooperative decisions in private than the sharp press reports would suggest. It’s all part of a delicate process of signaling and negotiation, but that doesn’t mean the issues can be fudged.

[The ISI official said Tuesday: “It seems that we are heading in the right direction — that is, the need to work together is far bigger than incidents like RD, but I think U.S. needs to do more in making this relationship grow on the basis of trust, respect and equality.”]

Over the past two years that I have been interviewing ISI officials, they have made the same basic point in every conversation, which is that Pakistan wants more respect and openness from the U.S. side as part of its cooperation in the joint fight against Islamic extremists. It has been a mistake to duck that issue in the past, and it would be even dumber now. There’s always a gap between what the ISI puts out in news leaks and what it does privately, but that gap is narrowing. That’s probably good for both sides. Less hypocrisy in the U.S.-Pakistan relationship is better for both countries.