I hate to ask, but you aren't wearing underwear under the shorts are you? If you are, don't.
How do you wash your shorts after riding? (I'm assuming that you wash them after every ride.) Sometimes hand washing doesn't work too well. I machine wash on gentle cycle and cold water using a mild detergent. Hang dry.
You might want to consider pre-treating the area before riding. I know people who use a baby diaper ointment before riding.