How could a bunch of 11 year old girls keep the secret....

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Krissi said that she had had sex with Ben when she was in pajama party with her friends. and they told it later to their friends/parents. So there was several days between said intercourse. And also lot of those discussions were rumors that he had molested several kids. Because Ben was convicted for a murder, there was no reason to put children thru that molestation case. And molestation wasn't main issue in this book.

As other poster said, there is no way to see who have lost their virginity with penis and who haven't. Someone have lost their virginity riding a horse, others dancing, using hairbrush to masturbate etc. And I'm quite sure if Krissi has been fantasizing sex with Ben, she has also fondled herself a lot.

Also cases with children are so sensitive that they don't want to do vaginal exams very easily unless there is certainty to find relevant evidence, so close proximity of said action.

What I want to know is why he and his gf would immediately run away with him knowing he was innocent. But then again look how often males go to jail based solely on a lying female's words, so.... since it doesn't take proof to have that happen, I guess I understand why he agreed to that running away plan.

This happens all the time in real life and the simple answer is that people want to believe (and protect) children, particularly girls.

they didn't keep the secret for 20 years - after the murders (which only happened around 12 hours after the lies about Ben blew up), the girls all got so scared that they'd summoned something supernatural that they all told the truth.
Krissi's parents never trusted her after this though, the family moved away but soon broke up, Krissi's descent in to her adult life as a stripper had begun, and so, on the rare times she was asked about it, adult Krissi would blame Ben for ruining her life and once again exaggerate the stories. Not sure what happened to the other girls.

There's a lot more circumstantial evidence about this in the book too, which doesn't seem to be fully explored in the film - when Ben put the "provocative" note in Krissi's ("cubbyhole" sounds wrong here!), a teacher saw him, and saw that he had a boner while doing so (which he had because he was thinking about sex with Diondra at the time), and he then lied that he was there to leave something or get something for his sister., which only made him seem more guilty.
They found animal....parts....in his locker (which Diondra had put there), all of which pointed to him being a depraved Satan worshipper who wanted to sacrifice children.
Worst of all, the detective told Patty that the accusing girls had said he'd kept their underwear as souvenirs - unbeknownst to Patty, Ben had recently brought a bag full of second hand small girl's clothing for his & Diondra's baby. So when Patty found this in his room, she feared the worst and had to believe that he really was going to go to jail as a child molester.

The molestation rumours were kept out of the trial - in the book, Lyle explicitly states this when talking to Libby - says the only good thing Ben's defence lawyers did was successfully argue that the 2 were unrelated. And by then it didn't matter because he's going down for life for triple murder anyway.

Of all the tragedies in the book, that Patty died believing her son really was a child molester is possibly the worst of them.