How long after the second course of antibiotics did you tested, as there is the possibility of a false negative if it was too close. The rule of thumb for chlamydia is three consecutive negative tests spaced a month each before you can be considered cured.
1. If there is no coinfection with a different microorganism then the most likely explanation
2. Chlamydia causes epithelial and nerve cell damage, and a persistent inflammation so give it a bit of time, for the symptoms to subside. Take a lot of fluids, calendula officinalis tea helps alot, garlic also.
3. And when you are at the urologist ask for a full bacterial panel.
Be disciplined in mind and body and best of luck.