One of the more common reasons for stones in the semen are prostate stones. I am going to forward an explaination from Dr. Richard Alexander, a urologist at the University of Maryland.
"Stones in the prostate are very common. They appear to be calcified proteinaceous bodies called corpora amylacea. The are thought to occur because the secretions of the prostate cannot get out of the gland because of the disarray of the architecture of the ducts due to BPH or benign prostatic hypertrophy, an almost universal growth of the prostate in men as they age. It is thought that these secretions dry out or become "inspissated" and form into a round proteinaceous body, much like a pearl in an oyster. They then become calcified.
This is not the only mechanism leading to the formation of prostate calcifications. They may appear secondary to an infection with insufficiently drained pus and detritus, eventually calcifying. Other calcifications, usually more widespread, can show up in the tissue surrounding the prostatic glandular units following an inflammatory process associated with tissue destruction or changes in the local biochemical environment (acidity, electrolyte changes). Finally, calcifications detected in the prostate can be located intraluminally inside the ejaculatory ducts, resulting from calcification of detritus in the seminal tract, eventually moving down into some narrow segment of the ejaculatory duct.
Prostatic stones are very common and generally do not cause symptoms in and of themselves but may be associated with the symptoms of BPH which men can get as they age and their BPH progresses. The stones are usually located between the BPH growth or "adenoma" and the compressed, normal prostatic tissue around the adenoma which is called the "surgical capsule" of the gland because it is the limit of resection of BPH when performed transurethrally. Stones in the urinary tract are completely different. These stones are found in the kidney where they form and can cause symptoms when the stone "passes" by moving down the ureter, the muscular tubelike structure that connects the kidney to the bladder. The presence of the stone, if it is large, in the ureter causes blockage of the ureter and "urethral colic", a spasm type pain that is severe and is often described by my patients as the worst thing they have ever felt in their lives. Kidney stones form from the urine and are often associated with some sort of metabolic problem that predisposes the patient to forming stones but this is not always the case of some patients simply form stones for no reason that can be elucidated. Kidney stones can sit in the kidney for years and not cause symptoms but can become infected and be a persistent nexus or source of infection for years. Typically infection stones are a different type of mineral and the infection cannot be cleared without removing the stone. It is possible that prostatic stones could be the same, that is, they could serve as a source of persistent and recurring infection in prostatitis. The only thing that makes me less enthusiastic about this possibility as an explanation for the relapsing and recurrent symptoms of prostatitis is that so few patients with prostatitis have a bacterial infection documented to be present in the urine or prostatic secretions. In large series of men a bacterial infectious etiology is found in only 51% of men. Unfortunately, urologists have concentrated on this subpopulation because it represents something they can treat but still does not appear to be relevant to 90% of men with the symptoms but no infection.
Many patients have had symptoms and several courses of treatment long before a culture has been attempted. The microorganisms may have been killed, but, without removal of obstruction, the inflammatory process may continue in the affected gland. This chronic inflammation may, eventually, live its own life, either due to persistence of highly resistant clones of microorganisms in low concentration and/or inflammatory reaction to products of the immunological defense mechanism and/or inflammatory reaction to glandular secretions/pus/detritus which cannot escape. Therefore, cultures from prostatic expressed secretion may not yield a positive result. Furthermore, even in presence of microorganisms in high = culturable concentrations, the culture may be (permanently or temporarily) negative if the process is sealed off by a stone or scar tissue."
Followup with your personal physician is essential.
This answer is not intended as and does not substitute for medical advice - the information presented is for patient education only. Please see your personal physician for further evaluation of your individual case.