ISI to a very large extent autonomous from Pakistan's military. Check.

"A simple fact of life in Pakistan is that even though the ISI was created as coordinating intelligence agency for the various armed services, it remains distinct from the army and to a very large extent autonomous from it. "
-- Abhijnan Rej, writing for Wikistrat on Pakistani terrorism

"Long feared as a blunt instrument of army power, the ISI has undergone unusual turmoil over the past 12 months."
-- From July 31 New York Times report on ISI's new chief; report filed by two veteran war reporters, Declan Walsh and Mark Mazzetti, who have long had extensive contacts in Pakistani officialdom

July 31, Pajhwok Afghan News:

Pak Army behind incursions, Senate informed
By Abasin Zaheer

KABUL - Senior security officials on Tuesday informed the Senate that cross-border attacks into eastern Kunar province were carried out by the Pakistani Army and intelligence service.

Over the past one year, hundreds of rockets and missiles have been fired into several districts of Kunar, killing and wounding dozens of people and forcing hundreds of families to flee homes.

Interior Minister Bismillah Mohammadi, Chief of Army Staff Gen. Sher Mohammad Karimi and National Directorate of Security deputy head (operations) Dr. Zia appeared before the Meshrano Jirga to brief lawmakers on the incursions.

Mohammadi said so far one thousand rockets had been fired into Dangam, Narai, Sarkano and Marawara districts of Kunar. A government delegation found the Pakistan army and intelligence were behind the attacks, the minister added.

“Heavy weapons with the Taliban are B-1 missiles, machine guns and mortars. The rounds of rockets we have found are available only to Pakistani forces,” the minister explained.

Pakistani Prime Minister Raja Pervez Ashraf, who visited Kabul earlier this month, said there had also been attacks from Afghanistan into Pakistan -- a claim rejected by Mohammadi.

The minister insisted that Afghan forces were ready to give a tit-for-tat response to Pakistani attacks, if allowed to do so. “It does not matter if we don’t have heavy weaponry; we have the spirit to lay down our lives for the country.”

Mohammadi accused Pakistani forces of encroaching on Afghan territory over the past three decades.

The chief of army staff said there had also been attacks from the Pakistani army and intelligence operatives in southeastern Khost, eastern Nuristan, Nangarhar and southeastern Pakia and Paktia provinces.

Gen. Karimi said information about the shelling was shared from time to time with foreign ministry, intelligence service and foreign troops. He said he had repeatedly asked foreign troops for a response to the attacks or their prevention.

“But foreign troops, particularly Americans, are not willing to prevent Pakistani attacks, fearing the closure of the NATO supply routes and the atomic bomb that Islamabad has,” he said.
[...]

There is no daylight between the ISI and Pakistan's military. Yet it seems the U.S. military would prefer to assume there is.