There is a thread on here somewhere (there are loads on water leaks I know) with photos that helped me sort my car out. Unfortunately I can't find it now for the life of me!
Anyhow I had exactly the same problem. I went through the whole sealing the 'plastic buttons' (the tailgate rubber bump stops shut against them) with silicone to no avail, alomg withe checking the lights were in properly, everything. Eventually I stripped all the trim out and discovered that it was getting in where two seams meet inside the rear n/s wing (a bit difficult to explain without pics I know).
The thread I now can't find with the identical symptoms showed that the water was getting in through a pinprick hole under the roof rail trim (run along either side just behind the door). I prised the trim panel off on both sides - i did so carefully and they just popped off, couldn't see anything obvious but siliconed all around the seam there between the side panel and the roof. The upshot is that cured the leak 100% and I had been getting it pouring in.
Hope that helps.