Cherokee,Air conditioning smells bad when car enables autostop feature

I am noticing a musty, foul smell from my air conditioning when the auto stop feature is enabled on my car. I have noticed that the air doesn't stay as cold, but while the air is blowing and also right after the car starts back up (after stopping), the air smells musty. Then, the smell goes away until the autostop enables again. My car has about 6,000 miles. Could this be the cabin air filter?