[Sci-Fi]

Sounds like mold, mildew, and/or fungi started growing in there. There are A/C disinfectants you can buy and use to spray in there or on the evaporator core. Some contain enzymes or chorine to kill the mold. If you are under warranty, take it to the dealer and have them take care of the problem. Here's pretty much how it's done (some are sprayed thru the center vents): http://www.georgenitta.com/../Evaporator.htm

It's too late now, but adding a cabin air filter (filters out dirt, mold, spores, and dust before they can collect on your evaporator core or enter the interior of your car), turning off the air conditioning a few minutes before you reach your destination and set the fan on high/defrost setting (dries out the evaporator core) will help prevent getting A/C smells. Some car manufacturers now have the fan or add a fan that cycles every 30 secs to dry out the evaporator core after the car is turned off. In extreme cases (dealers point of view), the evaporator core is removed and cleaned/replaced or even sprayed with a protective coating. But that is labor intensive.