Engine Cooling System problems of the 2009 Volkswagen Rabbit

I own a 2009 vw Rabbit. About a year after owning it, I started noticing a moldy smell in the car every time I turned on the air conditioner and/or the heat. I took the car into the dealer and they said there was mold in the air conditioning unit and they would clean it. When I picked it up, I asked what was the problem, and they said I need to turn off the defroster/air conditioner a few minutes before turning off the car so any moisture drains out. In essence, there is no cure, just a fix. I wasn't happy with the response. When I entered my car to leave, it smelled from some perfume they used to mask the mold smell. I am allergic to mold and mildew and have a variety of allergies. I had to leave the car windows open for a week to get rid of that odor. Now that it's fall, the weather is cooler and I'm using the heater. Although I haven't noticed the mold smell yet, I'm noticing headaches and sinus problems since I've been driving with the heater. I've driven american cars for 45 cars and never experienced this problem. I like the car otherwise, but cannot tolerate this problem. Why can't it be fixed permanently? I noticed complaints about the problem going back to at least 2002.