I'd say maybe heat rash that is only occuring at "stress points" like where the seam presses into your skin. How about trying a bit of powder on your skin there when you ride, or some sort of soothing lotion? Has the weather been hotter than usual when this happens?
Try washing the shorts in a mild diluted baby shampoo or something to see if that makes a difference. Sometimes things that don't normally irritate our skin will get irritated under hot sweaty circumstances.