I had bad problems with them a while ago. Shortly after, I was also having saddle issues too, and I never connected the two. So, I did all of the usual - got out of my shorts as soon as possible (although it was usually about 40 minutes after my ride, after I drove home) washed shorts before wearing again - in the machine because I wondered if handwashing was doing the trick, showering as soon as possible and staying as dry after - used baby powder (with cornstarch, NOT talc) and went commando, if possible. I also religiously use A&D zinc-oxide cream in the problem area before I ride. I don't know if I need to do this, but since I've started, I haven't had an issue.
I used acne cream to clear up the ones I had when I was having this problem.