water leaking into car when raining on 2006 Pontiac Torrent

my sunroof drains were clogged and water poured into the drivers side from the roof, took it to the dealer and they cleared the lines but since then every time it rains water is now coming in from somewhere into the car onto the floor mats. When you look under the hood there is rust where the water should drain so I am assuming those lines are also clogged but that didn't start until they fixed the sunroof. I am wondering if somehow they knocked these lines out of whack or something. They also charged a huge amount of money to blow air thru the lines. I'm taking the car in for service and don't want to be taken advantage of.

Asked by for the 2006 Pontiac Torrent
I see this is from 2010 but was curious if you found the leaking problem. My leak was from the sunroof also but all they had to do was reseal it and it's been fine