I had the same problem with my back headliner being soaked which led to my seat being wet :(
Mine was the top of the seal around the back window. I used to have a visor on the back when I bought the truck. When I got a camper shell, the visor had to go. Started leaking. My seal looked good but it was the culprit. We used a big spackling tool to bend the seal back and put a nice bead of silicone down through there. Hasn't leaked for a year now.