It depends on how soon after being treated you were tested again.
The chlamydia NAAT tests are really sensitive and it’s possible to get a false positive result if you get tested too soon after your treatment. The test could show a false positive result if it picked up some of the dead genetic material from the chlamydia.
We recommend that people wait 4 weeks from when they started taking their medication before doing another chlamydia test.
I don’t know your full situation to give you specific info for example how soon after treatment did you get tested, is there a chance you could have been re-exposed to chlamydia with an untreated sex partner etc.…, but if your first repeat test was done within the 4 weeks after treatment I would suspect that it was most likely an invalid test.
If you are concerned about the chlamydia being there I would see your doctor again and discuss about doing a test after the 4 week mark.
Let us know if this does not answer your question or if you have any more questions or concerns.