That's a tough case. You could very well just have prostatitis, even non bacterial. Or it could be one of the STDs not normally tested for, which are Ureaplasma, Mycoplasma, and Trichomonas. Trichomonas typically does not cause symptoms in men, but it's a pretty common infection generally.
Here is something I wrote up a little while ago about Ureaplasma and Mycoplasma which I will just copy/paste:
There at 3 types of mycoplasma to be concerned with for STDs, these are mycoplasma hominis, mycoplasma genitalium, and ureaplasma urealyticum. You can be tested through LabCorp, http://www.labcorp.com/datasets/labcorp/html/chapter/mono/vm003300.htm. It is often not covered by insurance. It is a urine based PCR test, and it is very accurate. You can also test through swab which might be more accurate, but obviously less comfortable.
About 40% (or more, and this number varies) of sexually active males carry ureaplasma urealyticum, so if you test positive that does not mean that is what is causing your problems. However, this organism has been associated with NGU in males and PID in females, as well as other disorders.
Mycoplasma hominis is less common, but still very common. Possibly just less than 10%. It has weaker ties to disease but some people still believe it to be important.
Mycoplasma genitalium is still less common, but it is a known genital pathogen. Although it's not tested for in your typical panel of STD tests, it seems there is more evidence linking this to disease than the other mycoplasmas. If you test positive for this, you should pursue treatment. Of course some will even debate this assertion, but this is my opinion. Dr. HHH considers this something which should be treated.
These organisms are frequently transfered at the same time as the better known STDs like gonorrhea and chlamydia. Gonorrhea has a high cure rate of about 98% (except for resistant strains, where cipro might fail but cefiximine will nearly always work) and chlamydia 96-98%. Unfortunately cipro is still prescribed often for gonorrhea even though it is now recommended against as treatment in areas with high resistance (West coast, Hawaii). However mycoplasma recur about 20-60% of the time. So recurrent urethritis is nearly never due to gonorrhea or chlamydia, unless the patient was reinfected.
Mycoplasma are harder to eradicate for a few reasons. Many strains are resistant to antibiotics, especially tetracycline resistance. This means doxycycline, a commonly prescribed drug, will often fail in treatment. Resistance rates of 50% have been reported for ureaplasma and doxycycline. M hominis is resistant to erythromycin, azithromycin, and clarithromycin. Levofloxacin, another common drug, also has been shown to have a high failure rate for M genitalium. This is why knowing which infection you have is very valuable in determining the correct treatment.
Another common phenomenon is to have treatment initially be successful with antiboitics, only to relapse later. This is because something like 1g of Azithromycin will often lower the amount of an infection without clearing it completely, so the bacteria will regrow over the course of the next few weeks (2-4 weeks is common). If the patient is retreated with the same ineffective treament, the same thing will often happen.
Since testing/treatment is not as common as for other bacterial STDs, treatment procedures are not as well known. Newer drugs such as clarithromycin and moxifloxacin show higher activity in vitro (test against cultures), but they are not prescribed as commonly. Since resistance to moxifloxacin is uncommon, this is probably a good choice for a second course of treatment where the first course of more common drugs fail, but once again due to limited data this is an opinion and not well proved. Erythomycin is the more commonly stated drug of choice, but it is less effective and has a higher profile of side effects.
Do I think that's what you have? Not necessarily. But you could. Is it worth it for you to get tested? That's up to you. Most doctors don't even know about these tests, so it will be hard to find someone who will listen to you.
My own experience was with all neg tests until I took one which turned up Ureaplasma, which had lived through 7d 100mg 2x doxycycline, 400mg cipro, and 1g azithromycin.