I have a 99 Civic hatch with a leaking problem as well. I found the problem to be at the tail lights. Water was coming from the roof through the channel of the hatch, hitting the foam that "seals" of the tailight, and coming right into the car. To check: open the hatch and pour water down the channel. It should take the path that goes around the light and onto the ground. If it comes into the car... there is the problem.