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Urethritis for 3rd time, no STDs, any ideas?

I'm a 39 year old male. Three times I have had bouts where I have a white pus-like discharge from the penis, accompanied by internal irritation. No pain or difficulty during urination or ejaculation. It happened at intervals of 2 1/2 years, then 7 months. All three times I, as well as my female partner have tested negative for all STDs. The urologist said to try diflucan first to see if it is a yeast infection, then  if the symptoms persisted, take medication for possible trichomoniasis infection. If that didn't work then he would have to do a visual inspection with a camera scope. I took a test for trichomoniasis (urine NAA test) and that came back negative as well. My last 3 partners have also tested negative for all STDs, including trichomoniasis. I had a rather complete urinalysis done and the only thing found was a trace amount of leukocytes. All other levels (pH, p rotein,HSV, urobilinogen, etc. normal). This last time I noticed  a few tiny, white, square shaped particles came out and within an hour the discharge turned clear and the irritation lessened dramatically, but was still present. The discharge quickly stopped altogether within a few days,with 2 times where I noticed a very small amount of white discharge at tip of penis when I woke up. I was put on a 7 day regimen of diflucan and symptoms went away by day 6. The previous two times this happened I took the standard std regimen of the shot and the pill. All three times, the episodes have lasted approximately three weeks, then they go away. Now I don't feel any of the original symptoms. I have noticed a slight amount of clear moisture inside the urethra, which I think is normal. No sign of any color. No sign of internal irritation. I have had a few incidences of itching EXTERNALLY on the shaft of the penis and a very slight patch of something rubbed off that looked like a small amount of dried soap. This happened towards the end of the diflucan treatment. It felt a little sensitive, but has gotten better. The other thing that happened one time was I noticed my urethra seemed kind of stuck together an hour or so after ejaculation. I think it was residual semen. Again though, no other discharge at any time.

What I want to know is if I am cleared for sex. The urologist said it was okay if symptoms go away, but I am very scared of there still being something there because this has happened three times now. Will condoms be enough protection? How long should I wait to confirm the symptoms are gone? It's been sevendays since I took the last diflucan pill and everything looks fine. No internal irritation or discharge at all. I have felt a few itchy spots EXTERNALLY, but the spot moves! I don't see anything and it's not constant or consistent. I try to wash with soap and rinse well. Right now I am noticing EVERYTHING and I'm paranoid in the extreme. If his was a yeast infection, how do I get them? I asked the doctor and he said it happens with people with compromised immune systems, but I don't have that. I have had autoimmune problems though before (demyelinating episode similar to MS, but only one lesion 10 years ago). Could that have anything to do with it?

If anyone has any advice, I would love to hear it.

Thanks!

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