water from a leak higher up in the car will always end up in the footwells, windscreen rubber or heater matrix/hoses for example. Might be worth checking underneath that floor-pan for damage,rust or holes where the rubber blank(s) has come out of. You can buy new blanks for the holes but if its rust or damage you'll need to glass fibre or weld sheet steel over it. Hope thats some help.
Chris P.Duck
February 2010