Both scenarios can happen. It is possible for her to have chlamydia all that time as well as catching it elsewhere.
Discharge can happen with a variety of infections and STDs. I would ensure that gonorrhea and chlamydia are excluded via urine tests or urethral swabs.
You can also consider having the prostate evaluated - since this can also lead to the symptoms you are describing. A digital rectal exam to send off any fluid to the lab for analysis and culture can be considered.
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