Your symptoms and the description overall are consistent with nongonococcal urethritis (NGU). Chlamydia causes 20-40% of cases, but the causes in the remainder aren't certain. It's an STD, so your partner(s) need to be examined and treated.
Doxycycline is one of the standard treatments, but treatment failure is pretty common; up to 20% of men have a relapse after the first course of treatment, just as you experienced. Chlamydia always responds to doxy, assuming you took the full 7-days treatment, and the standard chlamydia tests are highly reliable--so you can be certain that's not the problem. If you resumed sex with an untreated partner, maybe you were just reinfected.
Ciprofloxacin isn't the usual treatment for recurrent NGU. CDC recommends, and I endorse, that when doxycycline fails, patients should be re-treated with a combination of azithromycin (Zithromax) and metronidazole. Together these drugs cover some of the possible causes that are resistant to doxy.
The terminology you use to describe your doctor's advice, as well has his choice of the wrong treatment for your relapse, suggests he isn't up to speed on STD issues. You may want to get a second opinion, either from an infectious diseases specialist or at your local health department STD clinic.
Good luck-- HHH, MD
I just want to ad to my posting that I didn't have any kind of sexual intercourse since this infection started, so being re-infected from my partner is not possible.
Thanks
Alex68
Alex, how noticeable is the discharge?