It could be from the air conditioning.. They can get musty smelling from mold growing on the evaporator. The evaporator is always wet when the AC is in use. If the drain under the evaporator gets plugged, then water can sit in your plenem and breed nasty stuff.
If your heater core is leaking, you can also get a rubbery smell.. Run your finger over the windshield. If there's a light oily film there, you could have a leaky heater core......
Here's a quote frome the link I put at the bottom of this message. It deals with mold:
TROUBLESHOOTING AIR CONDITIONING ODOR
"If a vehicles air conditioner blows out air that smells like the inside of old gym sneaker when the A/C is turned on, microbes are growing on the evaporator. Mold likes damp, dark places. Bacteria can also thrive under such conditions. Besides smelling bad, it can be unhealthy to breathe (ever hear of Legionnaires Disease?).
To get rid of the unwanted organisms, various chemicals can be sprayed on the evaporator directly or through the blower ducts or air intake. Many replacement evaporators have a special chemical coating that inhibits the growth of mold and bacteria. The drainage tubes that carry condensation away from the evaporator should also be inspected and cleaned".
http://www.aa1car.com/library/ac98.htm