I don't think that a follicular fungal infection is out of the realm of possibility, make sure you have clean shorts every time, some people treat their shorts like delicate flowers so they may not get a really good wash, consider using some oxyclean and let them sit in the sun (the chamois part) to try and nip anything that might live there, another consideration is MRSA, or that you really have cysts not sores or pimples. I would get your doc to do a swab during your next active occurrence. Chicks get Bartholin's cysts but I don't think blokes have that issue, but it is similar to your complaint. Use an antibacterial wash after riding, keep your shorts really clean, consider a cream that has active properties, I really liked A&D diaper cream, but now I make a lanolin based cream with lavender oil. You could try using some neosporin if you are not fearful of resistant infection, but the swab would be the first move because if it is fungal, that should be an easy enough fix, as long as you and your shorts are treated.