I am having the same issue as seen in this thread:
The dealership couldn't figure out where the water was coming from and just dried out/cleaned my car without fixing anything. It appears to be coming from under the trunk liner and it is already starting to get more moisture/water just a few days after it was cleaned (only drove 10-15 miles since then).
Brand new car bought in May 2013 that smells terrible even after the dealer removed the water and cleaned out the car. Hope this gets fixed the next time I bring it in...