if the membrane between the door trim panel and door itself is,missing/damaged/or not stuck to door on at least the sides and along the bottom then water will enter footwells, as the water will enter the wrong side of door seals! hope this cures your problem,also it may only be front doors at fault the water will travel along floor to rear.[front doors more likely to have been worked on as they have key operation to locks.]
k
April 2010
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