I would suspect the weatherproof (ahem) sheets in the doorcards if the door seal looks okay
Remove the plastic trim cover at the bottom of the door frame and pull back the carpets and sound deadening to reveal the floorpan. Dry the sill, seal and floorplan so everything is dry.
Close the door, and pour a jug of water over the window of the door. Give it a minute, then open the door.
The weather-proofing in the door should ensure that any water running down the window and into the door, drains through the bottom of the door onto the sill. It there's any water resting on the door seal or inside the car, then the weather-proof seal inside the door is at fault.
Follow the guide in the link in the post above to fix it.