roof leak

According to many things that I read on the subject there are three things to look at. One is rust on the under side of the car. Two, is the rubber seal that you have addressed and the third is the seams of the sheet metal. They may look tight but they are often the culprit. Locate any seams and apply a coating of clear silicone sealant. See if that takes car of your problem.

is the water puddling up in the trunk, can you see where it is coming from, if lid and upper inside of trunk looks dry, do you have power antenna, sunroof, if so then there should be a drain tube for it and if the antenna is in the trunk the drain tube might have come loose and is draining into the trunk.
just 1 possibility

One source of water leaking into the trunk on Japanese cars is the gasket between the body and the rear tail light assembly. They seem to dry up and shrink and this open up gaps allowing rain water to get in. Remove rear len assembly and inspect and chaulk as necessary. This should help. Also, under the spare tire you will find some knockout or plugs to drain the water already in the trunk. Remove them to drain/air dry the trunk to keep it from getting moldy.