it could be coming in at the back and running under the seat belt reel and behind the carpet into the corner.
if you look where the roof meets the bodywork near the seat belt reel, there's a rubber seal at the end of the semi circle rear section which should channel any water out the other side of the door seal, if this has moved it does the opposite and channels it inboard.
I'll take a photo tomorrow to show the bit i mean
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