I haven't watched the episode yet so I'm going off of the summary. Jack should have known he raped Kayla. He read his own book! It was in his book because JJ got so upset finding out his father was a rapist that he shattered the store window in the square.
Jack raping Kayla wasn't in Jack's book. His book was about when he was held captive.
JJ was talking to Adrienne and she slipped (but not about what actually happened). JJ then confronted Kayla, who told him the truth. Later, JJ was in Horton Town Square, saw the display with Jack's book and his picture, then tossed a chair through the window.
http://www.salemspectator.com/threads/days-of-our-lives-mon-oct-7-2013.23019/#post-459114
Actually, it started a few days before, when Kayla slipped and said Jack was no saint:
http://www.salemspectator.com/threads/days-of-our-lives-wed-oct-2-2013.22986/
JJ is in the park with Bev, talking of Daniel not telling his mom so far, and asking if he can crash at her place tonight. Nope, her dad just hovers over her all the time (oh, yeah, that is how she could stay out all night at Dan's place) Along comes Kayla, JJ gets rid of Bev, and talks to Aunt Kayla. She tries encouraging him to go home, his mom loves him, etc. He doesn't think so, but perhaps in a couple of days she will be able to listen to reason. Kayla asks where he is staying, he comments not in the park, against the law, asks if he can crash a few days with her & Joey.Kayla gently refuses, telling him to go home, but JJ starts in about the family all hating him because of Daniel. She denies that, he says he is sick of everyone thinking he is so great, he bets she does, too. Well, she does, yes, and he really begins rants about Dan, calling him names, Kayla is saying that is not true, but JJ just goes on and on, calling him a son of a ........., and how rotten he is, really gets on huge rant.
Kayla is getting angry as JJ just won't stop, talking of how great his father was, his mother just won't see that. Daniel would never measure up, is not half the guy his father was, certainly is no saint. Kayla, in frustration, blurts out, "Your father was no saint either, and I know that better than anyone.". JJ asks what she means. Nothing, forget it, forget I ever said that. But JJ is insistent. "Just what do you mean, my father was no saint. What is it you know better than anyone"
For the next few episodes, JJ was trying to figure out what Kayla meant, going online and asking relatives, which led him to Adrienne, as noted above.