There are actually treatments out there for this very problem. You probably have mold/mildew in your ventilation system. Someone should have an idea of where to get the stuff specifically for cars. What you do is open the hood to provide the best access to the plastic grate just at the base of the windshield. With the fan on full, spray into the grate so as to ensure that it goes into every portion of it.
Lysol would probably work, but it has viral and bacterial killers in it, and is probably not as strong as the special stuff when it comes to mold and mildew.
Hey, maybe call an automotive A/C service place and inquire about it there.