I have a 1998 Chevy S-10 PU with a standard air conditioning system that has recently been producing a soured, musty smells when operating. The smell tends to lessen when the system is operated for an extended period but is evident when used later.
You can try opening the hood with the vent system fan on high and spraying Lysol disinfecting aersol spray into the intake duct at the base of the windshield. If that doesn’t work, then you may need a product such as this http://www.ac-evaporator-cleaner.com/frigi-fresh-single.htm
Tester
Make sure the drain is clear. Make sure the air intake is clear of leaves and other debris. Leave your HVAC system “open” when you park. That means in any position except “off” and recirculate/max.
Post back if you continue to have problems.
I will add one more suggestion. Make sure the drain from the A/C is clear. When running on a humid day you should see water dripping out under the car in front of where the passenger puts their feet.