Had your problem on a W202, the cause was a gap between the rubber boot seal and the boot lid, at the top end, closest to the rear window, over time the rubber seal can sag leaving a gap between the rubber and the lid.
When washing or in heavy rain, water would cling to the underside of the boot lid at its highest point, gravity would cause it to drip down to the lowest point inside the boot lid,(still clinging to the underside of the boot lid) the boot inner lining never seemed to get wet, this adds to the confusion as to where the water is entering the boot lid.
Remove the boot inner lining for a few days and keep an eye on the boot inside of the lid, the cause may become apparent.
Dec