I've experienced a similar issue, but in my Miata. I was able to trace the issue to this (see below). For what it's worth, if you have a similar setup on your car...might be worth checking out?
The rubber gasket was completed dried out and useless...and I always ended up with wet carpet in the passenger footwell. I ended up using a silicone gasket maker (generously) to resolve the issue. It's been a month now and it's been raining, no more leaks in that area.