On some of the early saffs the boot curves a bit more than the aperture its supposed to fit - right under the rear window and water can pour in if its heavy - light water runs down the troughs as it should. Ford sent out a dealer note to lift the seal off and to add sealant under it to raise it slightly.

If sealant is there (usually black) its probably just lost its grip so the seal dropped back onto the ridge again. The official fix just wore out )

Good old Ford design mate