I'm not much help on how to fix this (I'm not the most technical) but there are a couple of potential reasons;
1) Prior to me buying the car the dealer fixed this for me. Basically one of the windows had slipped slightly on the runner...the dealer demonstrated that by pressing both the window down buttons together. One window always went down much smoother and quicker than the other. I wouldn't have noticed myself but as a result it also wasn't the tightest fit and would have leaked.
2) Check where the water is leaking in from. I noticed the other day one of the seals on the top of the passenger door was a little loose. Although hardlies noticeable the water did trickle in. This is now also fixed...temporally. I basically pinched it back to where it was supposed to be and it's been fine since. Imagine I'll have to use a light adhesive in future months to fullt rectify the problems.
I didn't have this problem much in Vegas, but I have encountered it more here just recently. I took some bearing grease and rubbed it at the points on each side where the pillar and the top meet. I haven't had an issue with it since. I'll add a pic tomorrow.