Prostatitis can be consider, and may be improving on the antibiotics despite negative urine and blood tests.
Sometimes, extended courses of antibiotics are needed to completely treat cases of chronic prostatitis - 4-12 weeks are not unheard of.
Imaging the prostate with a transrectal ultrasound can be discussed as well to exclude an abscess.
I agree with the cystoscopy to further evaluate the GU tract.
These options can be discussed with your urologist.
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.
Kevin, M.D.
www.kevinmd.com