Based on what you write, I have two contenders/guesses as to what could be your problem. I aggree with you regarding prostatitis and I would suggest being tested for prostatitis. Prostatitus is an infection or inflamation of the prostate, and it can indeed produce pain like you describe. Symptoms of prostatitus also include:
"frequency of urination, slowing of the urinary stream, burning with voiding or ejaculation, burning in the penile tip unrelated to voiding, sexual dysfunction (such as difficulty with erection), aching in the penis, testicles, and discomfort in the lower abdomen, low back, groin, rectum or perineum (the area between the scrotum and rectum - betwixt the "wind and the rain")."
It is one of the most common reasons for men to be seen. It is NOT associated with prostate cancer, and there is NO link between prostate cancer and prostatitus. This condition can be caused by chronic or acute bacterial infections, and most commonly, there is inflamation but no bacteria present (but the semen does contain products of inflamation). There is also prostodynia, which produces pain but no objective findings.
To test for prostatitus, an analysis of the semen is made, and often it can involve a prostate exam as well. In prostatitus, Treatment for this involves antibiotics for a few weeks. Medication can also be given to relax the prostate so it is not as painful.
Here is a helpful website:
My second contender is a condition called epididymtis which is an inflamation of the epididymus, the collection of tubes that transports semen from the vas deferens.As you have had this for three weeks, I would label it chronic epididymus. Acute epidydimitus tends to occur suddenly and resolve with treatment, the chronic condition occurs gradually. Generally, in acute epidydimitus the urine is infected, in chronic, it is not. The chronic case generally does not produce a red or swollen testicle, but signs and symtoms do include pain in the testicles. There can also be (but doesnt have to be) bloody semen, pain on intercourse, and in the acute case, fever and a penile discharge.
The most common cause for the acute case in men under 40 IS an STD, and I know youve tested negative. The chronic condition can occur after acute cases are left untreated, or for no reason anyone can find.
Chronic epidydiditis doesnt respond that well to treatment, unfortunately. Generally the mainstay is anti pain medications.
I suggest a visit to a urologist who can do further testing and follow up.
Here is a helpful link regarding epidymitus: http://www.mayoclinic.com/health/epididymitis/DS00603
I do think the epidymitus is more likely than the prostatus given your symptoms are mainly scrotal based.
I hope that helps you...