Question: Why doesn't Jarod just go to the FBI or police and say, "Hey, these people kidnapped me as a child and are trying to rekidnap me, please arrest them". After what he's been through I cannot think of any reason for him to protect them. Also, why, when he's pretending to be a doctor or some government official, does he run when Parker or Sam or whomever come to get him? If he's in a hospital do you really think they could just drag him out at gunpoint unnoticed? It can't be that The Centre had infiltrated all of these government agencies to such a high level, or how could Jarod continually pretend to be FBI, ATF, Justice Department and military personnel without being caught? Many times he actually worked in the offices of these organizations.
Chosen answer: Well, there ARE people at the Center he wants to protect: Ms. Parker, Sydney, and Broots. Plus, people with influence like the Triumvirate has could stymie any investigation. And telling the FBI would necessitate revealing who and what he is to them, and he might be afraid that the Federal government would treat him as a guinea pig/resource like the Center did. Presumably, when the Center sends out Sweepers, they're "disguised" as law enforcement officials, with official-enough looking credentials to fool the casual onlooker. And just because the Center might have influence in government doesn't mean they necessarily have actual agents present everywhere. Perhaps Jared, in his Pretends, has made sure he's "under the radar." Besides, Jared doesn't KNOW how far up Center influence goes - after all, he wouldn't still be searching for "the truth" if he knew everything about the Center and its influence, would he?
Answer: Jarod was kidnapped because he is a child prodigy. A super genius, like all the other children, who were taken by the Centre. They needed him to construct improbable theories, that have world wide implications. Assassination, terrorist threats and military coupes. At first they used it to help governments, but then realised it was for their own ends. Which is why he escaped and to find his family.