In Case 4, Something's Fishy, Stella Nickells is caught for killing her husband by a small detail she neglected to think of - the Algae Destroyer in the cyanide in the Excedrin capsules. In Chapter 4, Jacob is caught having moved Jess' body by a small detail he didn't think would get linked back to him - the ROYGBIV quilt.
Rich thinks back on Gracie, a girl who committed suicide due to her father molesting her and her mother not being there for her because her brother had Down's Syndrome. Rich tries to tell Gracie's mother after the funeral about what was happening to Gracie but she doesn't want to know. I think what an awful woman and think she did know something was very wrong to some extent. This could also be foreshadowing to Theo's acting out due to Jacob's taking more of Emma's attention. I don't think Theo is going to do anything to himself or others, nor do I think he killed Jess. I have a theory about what I think happened at the end of the post. I also don't think Emma wouldn't want to know if Theo was troubled. I think she genuinely hasn't noticed. Also, between Mark and Jacob, Rich isn't the best initial judge of character for a cop.
I don't understand why Emma takes Jacob in to tell his story about why the ROYGBIV quilt is on Jess without questioning him herself and finding out why. She's already aware that Jacob's AS might be interpreted incorrectly by someone not familiar with AS. It seems possible that she really thinks that Jacob might have killed Jess unintentionally. Maybe she doesn't ask him because she is scared of him or scared of what he might say.
This book seems to be set now, time-wise. Most people know something of what Autism is now. Rich seems to that Autism makes someone act differently, yet he completely doesn't take it into account when assuming Jacob's guilt. No further research to see what is normal acting for a person with AS.
Now for my current theory on what I think happened. Jess gets out of the shower, she reaches for a towel, and she's dripping wet. She sees Theo. She screams, maybe wraps the towel around her, and goes to chase Theo. Theo turns and runs out of the house, knocking into things and making a mess in his haste to get out of there before he's caught. Jess slips on the wet floor of the master bath (I remember either Jacob or the cops mentioning something about the master bath having been cleaned and I remember Rich mentioning it had be used recently), she falls, hits her head, and dies from the head injury. Jacob sees Theo leave and drop the iPod, which he collects. He assumes that Theo either saw Jess dead and that Mark had killed Jess or, correctly, that Jess had died accidentally. Either way, Jacob knows he needs to clean up the crime scene after Theo had been there so Theo isn't falsely accused.