I have a 2000 E46 323ci convertible that has water leaking into the trunk. It seems to be coming from the convertible top compartment but when it rains hard I get water coming off the inside of the trunk lid!!
It looks like all of the molding is soft with no cracks but when the interior of the trunk lid is wet it seems to be coming from the felt like molding inside of the rubber molding on the bottom of the trunk lid.
Also when this happened the lask time I noticed that the back side of the panel covering the convertible top compartment (like the back edge of the rear deck where the top meets when it is closed) was also wet. 





