GWEN IFILL: Next: a diagnosis reconsidered.

For decades, when a child appeared in an emergency room with unexplained head injuries and a disturbing set of symptoms, many doctors assumed one thing to be the cause: violent shaking and potential child abuse.

But, in recent years, the diagnosis — diagnosis of what's known as shaken baby syndrome has come under intense scrutiny, and so have many of the prosecutions and convictions that followed.

Special correspondent Jackie Judd begins our story in Olney, Maryland.

JACKIE JUDD: On a glorious Sunday last Memorial Day weekend in suburban Washington, Andrew Shortell taught his son, Piers, how to ride a two-wheeler.

MARIELLE SHORTELL: Go, go, go.

JACKIE JUDD: His wife, Marielle, happily shot the scene, with baby Tristan nearby. Later, the couple marveled at how complete their family now seemed.

ANDREW SHORTELL: It was just an idyllic, perfect weekend.

MARIELLE SHORTELL: Tristan was in a jovial mood. He was smiley.

JACKIE JUDD: Twelve hours later, their lives were unimaginably altered when Marielle realized 18-year-old Tristan had not cried out for his usual 2:00 a.m. feeding.

MARIELLE SHORTELL: I shot up in bed and looked at the monitor and all I could see was his butt in the air. So, I went into the room and I pulled him up out of the bed and I just heard this, like, gasp for air. And I looked at him, and he was so cold.

JACKIE JUDD: Marielle finding Tristan slipped over and struggling to breathe raced to this nearby community hospital. There, she says doctors thought he might be experiencing a diabetic reaction.

At MedStar Georgetown University Hospital, where the baby was soon flown, she says doctor suspected meningitis. By Wednesday morning, Tristan was dead. A doctor told the Shortells the cause appeared to be child abuse because of bleeding behind the eyes and other symptoms.

MARIELLE SHORTELL: And he pulled both of us into the psych room and he said: “We have reason to believe Tristan died from shaken baby syndrome. The evidence doesn't lie.”

And I think my mouth dropped. We're like, there's no way.

ANDREW SHORTELL: They said SBS. And I was, I didn't even know what that is.

JACKIE JUDD: Within minutes of Tristan's death, Marielle was put in a room and questioned by a social worker and a homicide detective. It was the start of a family tragedy and a legal nightmare, as well as a window into what some view as a deeply flawed process of diagnosing shaken baby syndrome, flawed because it is now understood that accidents, like falls, infections, blood disorders, even the birthing process, can cause some of the same symptoms once widely believed tied only to shaking.

KATHERINE JUDSON, University of Wisconsin Law School: We know it can happen from accidents. We know it can happen from disease.

JACKIE JUDD: Katherine Judson teaches at the University of Wisconsin Law School and consults globally on shaken baby cases for the Innocence Network.

KATHERINE JUDSON: There are still some doctors who believe that when you see a particular set of findings and you don't have the explanation of a terrible accident, like a car accident or a fall from a really high height, or a particular illness, that what must remain is abuse.

JACKIE JUDD: The set of findings or symptoms is often known as the triad, bleeding behind the eyes, bleeding around the brain and swelling of the brain.

For decades, some doctors have considered the presence of the triad as irrefutable proof that a baby has been violently shaken, as illustrated in this animation used in legal cases, causing the brain to slam against the skull, further, that the disabling and sometimes fatal symptoms come on so quickly, the last person with the baby must be responsible.

The most notorious case involved Louise Woodward, a nanny in Massachusetts, who, in 1997, was found guilty of involuntary manslaughter. More than 1,000 cases of shaken baby are diagnosed every year. Experts estimate that at least 100 of those are prosecuted.

JACKIE JUDD: Some of those convicted have turned to the Innocence Network's member organizations. That includes Drayton Witt, who lives in the Phoenix area. He is one of about 20 people who, with the network's support, have had their convictions overturned in the past two decades.

In 2000, Witt and then his girlfriend Maria were in and out of the hospital with her infant son, Steven, following a complicated birth. Witt was alone with the 4-month-old just before they rushed him to the E.R. for the final time.

DRAYTON WITT: Knowing that he had a medical history, knowing that he had a seizures, knowing that he had a very troubled history from birth, even knowing that, as soon as, you know, baby shaken syndrome was thrown out there, it was a train they all jumped on. Nobody decided to look any further.

MARIA WITT: If I felt for one millimeter of a second that he did something to our son, I would have took care of himself. And that's what I told the cops. Steven was my entire world. And if I felt at all he was ever in danger, I would have never put him in that situation.

JACKIE JUDD: Witt says he was an angry and aggressive young man who looked the part of a rough. Yet he was still surprised to be found guilty of second-degree murder. He spent 12 years in prison, until his appeal was heard.

In a statement to the court, the medical examiner wrote: “There is now no longer consensus in the medical community that the original findings I reported are reliable proof of shaken baby syndrome. I believe Steven's death was likely the result of a natural disease process.”

Since walking free in 2012, Witt with his now wife and daughter have been catching up on a life delayed.

DRAYTON WITT: My peak years, yes, are gone. Everything for me is starting over mid-30s. Some people don't recover from that, and that's something that needs to be not taken lightly.

JACKIE JUDD: Dr. Lori Frasier, an expert on child abuse, treats patients at Penn State Hershey Children's Hospital and teaches there at the College of Medicine.

LORI FRASIER, Penn State Hershey Children's Hospital: We have to be totally honest with parents what we're doing.

JACKIE JUDD: She has always believed the triad can appear for multiple reasons, but she also believes that in this contentious environment, the defense too often ignores the obvious.

LORI FRASIER: But when you have symptoms that could be due to severe head trauma, you have to investigate them, because that's our mandatory obligation under the law. The standard is reasonable suspicion, and those features do provide a reasonable suspicion in the medical setting.

JACKIE JUDD: No one disputes child abuse occurs. The issue here is how to narrowly identify the reason for a medical crisis.

How do you tell the difference between abusive and accidental?

LORI FRASIER: So, it depends on the severity of the injury, associated injuries, other injuries. We take a detailed medical history. We spend probably at least an hour or more with families going into detail. Tell us what happened.

KATHERINE JUDSON: I have a lot of respect for the folks who work really hard to figure out what the difference is, but we need a more accurate way of figuring out the difference, because it is absolutely unacceptable for children to be abused, and it is similarly absolutely unacceptable for people who did nothing wrong to be imprisoned for crimes they didn't commit.

JACKIE JUDD: Judson of the Innocence Network says, despite the evolving science, she has not seen a decline in the number of shaken baby cases being prosecuted, diagnosed and investigated.

That was the legal limbo Marielle and Andrew Shortell found themselves in immediately after Tristan's death. For several months, they were not permitted to be alone with the surviving son.

MARIELLE SHORTELL: It was awful. I couldn't sleep. I was depressed. I'm thankful that I have made it to this point, because there were moments where I was like, I would just rather go join him.

JACKIE JUDD: Most days, though, the Shortells soldiered on, packing up the rental house where they had so recently brought their newborn and moving to a place of their own.

A legal resolution of sorts came in December. The medical examiner ruled the cause of death as undetermined. Nothing in the autopsy report suggests signs of abuse, such as fractures, broken bones or blunt impact. However, the Shortells say the state of Maryland will not expunge records of the case for three years, and until then, they could be flagged for extra scrutiny, if they want to open a day care center, for example, or adopt a child.

ANDREW SHORTELL: Instead of grieving, you find yourself trying to defend yourself.

MARIELLE SHORTELL: I did feel we were guilty until proven innocent.

JACKIE JUDD: The Shortells have raised money in Tristan's memory to develop a guidebook for diagnosing shaken baby syndrome.

Ten months on, they try to help their 7-year-old adjust and to make sense of their loss.

ANDREW SHORTELL: You go through that anger, that first phase of all the sadness. I mean, you could through just incredible sadness and not understanding what's just happened to you. Then there's — then there was the anger at like these people that are now intruding into our lives and are looking at us like we did something that we didn't — that we know we didn't do.

MARIELLE SHORTELL: I remember on New Year's Eve, when the ball dropped, we just looked at each other and just burst into tears, just, like, oh, my God, that was a horrible year. Like, the first half was the best time, and then on May 26 at 3:00 a.m., our life changed.

JACKIE JUDD: And now, with the cloud of suspicion gone about just what happened that night, they are free to truly grieve for their little boy.

For the PBS NewsHour, this is Jackie Judd in Bethesda, Maryland.

GWEN IFILL: We asked MedStar Georgetown University Hospital and Maryland's Child Protective Services to comment on this story. Both declined to appear.