Same situation here: short drive and a short sit will "activate" the stink. If you pull the old filters out and smell them, they don't have much smell when they are dry. If they get just a little damp, they STINK. So I think what is happening is that condensation builds up when you take the short trip and just a few minutes sitting while you are out of the car allows condensation to drip onto the filters making them damp. Then when you start up, you get the activated stench. If you let it go for a while without replacing the filters and cleaning the coils, eventually the stink will make its way into the coils too. Not sure how to "fix" this. I wondered if blasting the fan at 10 for a minute before you stop might help push condensation out of the coils but I've not tried that yet.
Mike