I would continue to test for Chlamydia to see if it has been appropriately eradicated. Persistant infection would warrant evaluate of the prostate - which can be difficult to treat. I would suggest a thorough digital rectal exam with prostatic massage to culture out any prostatic fluid. You can also consider imaging studies of the prostate - such as a transrectal ultrasound - for further evaluation.
If negative, you can consider a cystoscopy to evaluate for non-infectious causes of the burning (i.e. a urethral polyp or stricture). This 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.
Medical Weblog:
kevinmd_b