Hi Tim,
I am having a problem that sounds very similar. For the past year or so, I have frequent discomfort in my urethra, and my opening of my urethra is often inflamed and irritated. One of the two sides of the opening of the urethra is protrudes up higher than the other side. I am in a monogamous relationship, and we have both been tested for every STD possible and came back clear. I even underwent an unpleasant peniscopy, which came back normal.
My urologists (I am now on my third for the same issue) have all said things look normal and assured me they don?t suspect an STD, cancer, or anything serious. I just went back to the urologist recently after trying to ignore the chronic symptoms for six months. He gave me three theories:
1) Just non specific urethritis, and he gave me antibiotics to hopefully help it clear up.
2) I may be allergic to the condoms, soap, or detergent I am using.
3) I could have very small kidney stones that are presenting symptoms at the opening of my penis. He used the analogy of a heart attack presenting with symptoms of pain in the left arm.
My personal guess is that it is theory 1, but I am less than optimistic that the antibiotics will work, as I tried them once before. I share your frustration, and the frequent recurrence after sex has made me lose sexual desire to a large extent. I feel your pain....