I have a 98 Saraha with the same problem.
All the weather stripping on mine is in excellent shape as well,
STILL...water runs down my back window just like yours.
I've had my TJ for over a year now and still can't figure it out.
At this point I'm baffled, and just put a towel back there when I know it's gonna rain.
If anyone has a fix, please let us know.