Here is an excerpt from the Haaretz article, auto-translated back to English:
Information about the Syrian nuclear program came to the Mossad by accident. A few years before, on Christmas Eve 2003, Libyan leader Muammar Gaddafi announced that he agreed to give up his plans to produce weapons of mass destruction. Israeli intelligence - the IDF Intelligence and the Mossad espionage agency - were stunned. They did not have a clue about the Libyan leader's intention , and they learned it from the media.I just ordered the book.
Dagan and research officers of the Mossad intelligence wing sank into a sad reverie. They asked themselves: "If we did not know about Khan's activities in Libya (Pakistani nuclear scientist, Abdul-Qadir Khan, was that brain behind the Libyan nuclear program), what else don't we know?" Consequently, in early 2004, the head of Military Intelligence demanded to examine every piece of information collected and stored in the last decade in connection with his actions, his conversations and Khan's trips in the Middle East.
Intelligence communities tend to store hundreds, if not thousands of bits of information, not always with the time and tools for humans to read or listen to them carefully. Information that is important can disappear because no one noticed it or people didn't understand its meaning. They found that Khan visited Saudi Arabia, Egypt and Syria. The evaluation was that because Saudi Arabia and Egypt are countries friendly to the U.S., they will not rush to accept the offers of Dr. Khan's services to purchase nuclear know-how. In any case, the Mossad assessed, even if they keep in touch with him, then the U.S. will know about it.
Therefore the Mossad decided to concentrate on Syria, a country hostile to Israel, who runs anti-American policy and that cooperates with Iran and supports Hezbollah. Bashar al - Assad, who took power after his father died in 2000, was inexperienced and may have been tempted to do reckless or adventurous acts.
A few months after the start of the initial examination, the spring of 2004, researchers returned to the Mossad's research division to their division head and told him that indeed there is something behind it, because as the intelligence division investigators pursuing the Mossad's issue, they found more and more suspicious and worrisome signs.
It turned out that Syria has increased three years prior to testing the secret dealings with North Korea. The Mossad had known about the cooperation between the two countries in the development of Scud missiles, but now there was also cooperation between them in the nuclear field.
(h/t Yoel)
UPDATE: Challah Hu Akbar notes another book that covered this topic, excerpted in JPost a short while ago. Each has details the others don't have.