Saddle sores are like zits. Don't know how else to describe it. They are very painful bumps - I had one that was more like a cyst and hurt, man did they hurt. I used hydrocortizone (sp) creme on them to reduce the swelling. They were caused by the seams of the shorts rubbing right at the join. The pad had worn thin and the seams were fraying I guess since they were just entry-level shorts and never meant for what I was using them for.

Just as a footnote: after every one of my long distance rides - I rode the next day with no "saddle" issues and commuted to work the following Monday. I actually started developing the saddle sores during one of my morning commutes so I had a chance to heal them and get new shorts before my next long ride. Thank Goodness! LOL

I would guess it's either your shorts or your saddle - especially if you're still having issues.