6 months ago I had unprotected sex with a girl (whom I've been dating since). About two weeks afterwards I developed swelling around the base of my penis. The swelling is difficult to desicribe.. it was under the skin and was hardened (not pus filled), and painful when touched. It never scabbed or became an open sore. The swelling went away after about three weeks, and later I developed two little red bumps, one on the base left side of the penis (almost on the srotum), and another on the pelvic area. Neither was painful, except when touched. Naturally I freaked out, and told my gf to get tested. We both got tested for "everything in the book". In my case that included, HSV I & II, Hep A & B, HIV, Syphilis, Gonorrhea, and Chalamydia. I had one of these red bumps during my blood test (which the doctor said might simply be a ingrown hair). The tests came back negative for me and my gf. So we though we were ok and kept having unprotected sex. After some time I noticed a pattern. Every time we have sex, I develop one or two little red bumps (and sometimes a little rash) 2-3 days later. They always seem to develop in the exact same area (I find this very weird) around the base (never on or around the tip. I also have never had any discharge or burning). They don't hurt unless I touch them and go away within a week. I went to a urologist afterwards. He looked over the test and said there's nothing wrong with me, and gave antibiotics. I haven't gotten the antibiotics yet.
What can this be? I'm extremely confused and worried. What other tests can/should I request to be done?