I had the same issue... since my driveway is on a downward slope, the water would find its way into the rear right passenger seat.
At first it was the rear window seal, replaced. Then the leak found its way halfway underneath the bootlid seal. If you lift the seal after rainfall, even after a day of drying, you'll still be able to pinpoint if the water finds its way underneath the seal.
Re-fit the seal nice and tight, maybe even add some rubber sealant such as Silastic.
I fixed this leak, and then the water started channeling down near the taillight to this circular black plug near the bottom left of the right taillight (remove the rear boot trim). The water would somehow leak through the top of the plug and into the boot again.
To fix this leak, remove the rear bumper and you'll even notice where the water has gone through and evaporated to leave a dust trail. Remove the black plug (push it out from the inside) apply more sealant, clean the plug and reapply.
My leak problem has been gone ever since, I've probably had about 4 or 5 big downpours in the last two weeks and no leaks
Let me know if you need pics
-az