The 10News I-Team first detailed San Diego's files in May and has now found cases where the Boy Scouts didn't tell authorities about the sexual abuse they had documented.
San Diego is home to at least 35 examples of alleged sexual abuse in scouting, the I-Team reported.
"Have you heard about cases of abuse inside the Boy Scouts of America before?" I-Team reporter Mitch Blacher asked.
"Oh, yes, yes," former San Diego prosecutor Phyllis Shess said.
Shess prosecuted sex crimes against children, including children in scouting.
In 1992, Shess prosecuted John Atwood, a man well known to the Boy Scouts who is now a convicted sex offender.
The Boy Scouts' file on Atwood documents allegations in August 1991 that he molested a scout in a San Diego hotel room.
"Did the Boy Scouts of America help you in anyway?" Blacher asked. "Did they alert that this was happening?"
"They didn't alert me," Shess responded.
"Did they alert the police?" Blacher asked.
"Law enforcement was alerted by a couple of the boys' parents," Shess said.
Since the Boy Scouts' confidential files from 1971 to 1991 were made public by court order, the Boy Scouts of America have declined 10News requests for on-camera interviews.
"We believe perpetrators of abuse should be punished to the fullest extent of the law," Boy Scouts of America CEO Bob Mazzuca said in a video produced by the organization.
Mazzuca talked about why the organization handles abuse allegations the way it does.
"We have kept these files confidential because we believe victims deserve protection and that confidentiality encourages prompt reporting of questionable behavior," he said. "It removes the fear of retribution and ensures victims and their families, the privacy they deserve."
A BSA spokesman told the I-Team the group's current policy requires everyone "involved in scouting to report to local authorities any good faith suspicion or belief that any child is or has been physically or sexually abused."
Despite the Boy Scouts' policy and Mazzuca's comments, some expressed a growing suspicion that protecting scouting may have been more important than protecting individual scouts.
"Certainly there is pressure on scout executives, as I understand it, to make sure membership levels stay up," Santa Barbara lawyer Tim Hale said. "Clearly, if an organization is talking openly about the fact that children are being sexually abused within it that at least initially could have a negative impact on membership levels."
Hale is trying to get the Boy Scouts to publicly disclose the files they continue hiding -- files dating from 1992 to the present. Hale is one of the only people who have seen these more recent files.
"One of the most disturbing things we've discovered is for decades they've been receiving reports of abuse and quite often not reporting them to law enforcement," Hale said.
Hale sued the Boy Scouts after former Santa Barbara scout leader Al Stein was convicted of molesting his client.
Stein, now a registered sex offender, was turned in by his victim's mother in Santa Barbara.
Hale said a scout executive tried to keep the case away from police.
"That scout executive attempted to prevent her from reporting that crime to law enforcement," Hale said. "If our client's mother had not resisted that attempt by the scout executive, Al Stein undoubtedly would be roaming the streets and he would have abused again."
The Boy Scouts spokesman denied discouraging anyone from reporting suspected abuse within scouting.
Some confidential files from 1971 to 1991 did result in criminal prosecution, the I-Team found.
Thomas Wood, Rodney Stark and Raymond Weeks were all San Diego scout masters during those years. The Boy Scouts kept confidential files on all three -- who are now convicted child molesters.
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Like hundreds of files the I-Team reviewed, the files on Wood, Stark and Weeks showed no evidence the Boy Scouts told police about the allegations.
The I-Team asked the Boy Scouts of America for specific examples where the organization alerted police about suspected abuse. The BSA has not responded to that question.
"We believe perpetrators of abuse should be punished to the fullest extent of the law," Mazzuca said. "Confidentiality encourages prompt reporting of questionable behavior."
Four years ago, Stein testified he never saw the scouts report any sexual abuse. On Wednesday, find out what Stein said under oath.
The I-Team's continuing coverage also reveals something the scouts didn't want the public to see -- an internal memo to scout executives which seems to lay the foundation for how scout's handled abuse allegations.