From your description, herpes sounds possible, but not very likely. Although your symptoms sound like they vary in severity, they have been there more or less the whole time for 2 months, which would be very unusual for herpes. And herpes in the urethra usually is more painful than you describe. Finally, you are right that herpes more likely would include external genital lesions. Completely asymptomatic genital herpes is common, but in men with symptoms, having symptoms only in the urethra is rare.
In at least 10-20% of people with nongonococcal urethritis (NGU), whether due to chlamydia or other things, the symptoms persist or come back. Also, there is a slight possibility your chlamydia wasn't cured; azithromycin (Zithromax) is good against chlamydia but not perfect. Trichomonas is a possibility as well. Gonorrhea is theoretically possible, but probably would have been picked up when chlamydia was diagnosed.
The standard approach to patients like you (as recommended by CDC and as we do in my STD clinic) is to first make sure that there is urethritis, easily done quickly by swab from a urine specimen; and also to re-test for gonorrhea and chlamydia. If persistent NGU is confirmed, you should be re-treated, usually with doxycycline, and perhaps also with a drug against trichomonas, just it case it is there.
Finally, I assume your sex partner(s) were examined and treated for chlamydia, and that you haven't had sex with anyone since your initial treatment. If the partner you caught chlamydia from hasn't been examined, that's important for her (or his) health--and the exam also might show something else that could explain your problem. And if you have had sex with that person or anyone else, that person needs to be reexamined now.
I hope this helps. Feel free to print out this response and take it with you when you go back to your doctor.
Best wishes-- HHH, MD
Paragraph 3, first sentence: that should say "easily done quickly by swab OR [not from] a urine specimen".
HHH, MD
Dr H,
You say "In at least 10-20% of people with nongonococcal urethritis (NGU), whether due to chlamydia or other things, the symptoms persist or come back."
For clarification, is it possible after initial exposure and successful treatment yielding a negative test result (say at 12 weeks) to have the symptoms come back (with no other possible exposures)??
Yes, that's entirely possible. It happens all the time.
HHH, MD