Urethritis due to other causes (e.g., Mycoplasma genitalium, Trichomonas vaginalis, or herpes simplex virus): This is a likely cause given the symptoms and the negative tests for gonorrhea and chlamydia. These pathogens can cause urethritis, leading to a burning sensation during ejaculation or urination.

Prostatitis: Inflammation of the prostate gland can cause burning sensations during ejaculation. Given the normal urinalysis, chronic prostatitis or pelvic pain syndrome could be considered.
Urethral stricture or obstruction: Any narrowing or blockage of the urethra could cause discomfort or a burning sensation during urination or ejaculation.
Allergic reaction or sensitivity: The patient or his partner might be experiencing an allergic reaction to a component of the semen, such as sperm itself or other substances present.

Cancer (e.g., prostate, urethral): Although rare, cancers in the genitourinary tract can cause a variety of symptoms, including pain or discomfort during urination or ejaculation. Early detection is crucial for effective treatment.
HIV or other sexually transmitted infections (STIs) not yet tested for: While gonorrhea and chlamydia have been ruled out, other STIs could be causing the symptoms. It's essential to consider and test for these to ensure proper diagnosis and treatment.

Semen allergy (human seminal plasma hypersensitivity): A rare condition where the immune system reacts to proteins in the semen, potentially causing burning sensations or other allergic reactions in the partner.
Ejaculatory duct obstruction: A blockage in the ducts through which semen passes can cause pain or discomfort during ejaculation.
Zinc deficiency or other nutritional deficiencies: Certain nutritional deficiencies have been associated with changes in semen quality or composition, potentially leading to discomfort during ejaculation.