Bright Red Urethra / Shorts bouts of Penile Pain after Intercourse (No STD)

About 6 months ago, I began experiencing a mild burning sensation in my penis. There were no visible sores/blisters/pimples/bumps/warts of any kind, but my penis just felt warmer than usual, almost like it had a fever. This progressed for about a week and I went to an urgent care clinic who did an exam and said they saw nothing wrong, but ordered blood/urine anyway. Tests came back negative for all STIs and no indications of a UTI present. It did not hurt to urinate, but it was uncomfortable/the tip stung AFTERWARDS and always felt like a bit of urine was left inside.

I went to a urologist who diagnosed me with prostatitis and put me on a cocktail of antibiotics. I've been on doxy, cipro, azythro, flagyl, and anti-fungals. All of them provided temporary relief, but the pain would return after the antibiotics were done. I was even put on a month and a half long course of doxy to no avail. The pain was never severe, but enough to worry me that something was wrong and no doctor could figure it out.

My symptoms were always a bright red urethra during erection, and my penis glans seemed swollen/enlarged. No pain during ejaculation, but some discomfort afterwards, and then everything went back to looking normal once erection faded. After a few more trips to the urologist they ultimately said it was most likely "Non-Sexually Acquired Urethritis" or "NSU" (Non Specific Urethritis) which they proposed was caused by normal bacteria that my body was reacting badly to, and that it had to run its course.

I started with some home remedies for prostate/penile issues - saw pallamino, cumin, those sorts of things - and slowly but surely the pain started to go away. I was finally starting to feel normal again after about 4 months of worry.

Over the course of 6 months, I've had multiple tests for every STD (Including HSV) and come back negative for everything. Negative for herpes, negative for chlamydia, negative gonorrhea, negative syphilis, negative HIV and negative for all Hepatitis strains.

Fast forward to now, my girlfriend and I started having sex again since I was feeling better. We had unprotected vaginal sex which we've had for  years, and then I put a latex condom on (which we've done plenty of times before) towards the end so we could - well, you know. 

Afterwards I went to the bathroom and had a small sharp twinge at the glans again during urination which quickly went away, but was obviously noticeable. I inspected the inside of my urethra and what-do-you-know, the bright red urethral skin was back again. It felt like I had urine stuck in the tip, blah blah blah. However, I've masturbated successfully for months now without this occurring afterwards. I know we don't have STDs because we've done all of the tests and we're WAY past the point where the tests would be accurate, but I can't understand why I'm still having this pain.

I realize I'm grasping at straws by coming here and hoping someone has an answer, but I'm at a loss and so are my doctors. Does anyone share a story similar to mine and have any suggestions? My girlfriend shows no signs or symptoms that anything is wrong, so it would seem clear that I don't have any infection (sexually acquired or otherwise) that I am passing to her, but it's just frustrating having this pain and redness after sex and not knowing why. This has never been a problem in my life before 6 months ago. I'm 30 years old.

Well that is something.  The only thing I could say is because you are able to masturbate without a problem.  Maybe your condom is to small or your allergic to the condom.  Has your girlfriend use anything in the vagina during sex.  Do you pee right after you come.  Sometime the sperm get stuck in the urethra and it will irritate it. I wish I can help you more  Good luck  Ken