I have a similar problem. About 3 days after a sexual encounter, I had 4 chancres which looked like syphilis, no blister and circular scattered at the base of the under shaft. It was painless and shallow in the skin. I applied neosporin and they went away in a week. A few days later it came back in various other areas on the shaft. Its stages were:
1. A red irritated dot on skin 2. Progressed to a dark-red circular scabbish crackling of the skin, looked like syphilis 3. Slow healing rate, three weeks later, as it tries to heal, the scar remains and is dark-red with minor "pinhole" cracks in it.
Three weeks later I went to the doctor, took a syphilis test, with normal results. I took doxycycline for a week as it seemed to be trying to heal, and eventually the dark scars turned to normal skin. A week later the last chancre that formed before came back, so I immediatly took a 2 week doxycycline med and got a herpes test. The test came back normal and after the 2 week treatment, they still remain and now over three weeks my under shaft has a 3/4 inch diameter dark-red circle of seemingly scar tissue with little pin holes in them. Ive stopped treating the problem and it seems to be healing at a rediculously slow pace, almost like it stopped. When I pour alcohol on it, its has a 8 second delay before I feel a slight pain. I think another patch of it is forming on the shaft and I am getting fed up. Anyone have any experience with such problems? Since the 3 doctors have no answers for me and are suggesting I have a biopsy (removed skin analysis....I dont want them carving into my tool leaving scars)