I was also plagued with water leaks in my trunk. I was sure it was unrelated to the black seal. I used some clear silicone on the cracked body putty areas from the factory and other problem areas others have pointed out. I then did the lock me in the trunk with flashlight routine. Water was coming in pretty quickly from inside the trunk from the bumper area. I removed the plastic liner that surrounds the front wall of the trunk and noticed a single bolt missing from the bumper area. Water was coming in this bolt hole! I siliconed and replaced, now no more leaks I hope!

Keith