You know, I've had the same problem but only during heavy rains (which we've had just one season in CA in the last few years). The carpet next to the driverside rear door gets wet. Hasn't been much of an issue so I haven't really bothered with it.
I'm definitely interested in hearing what the cause is though... my thought has always been that the outer window seal has somewhat peeled back because of age. I was thinking that water has been getting through there and leaking to the bottom of the door but I can't back that up in any way.