what you had was a UTI, and it's not always in your bladder, it coul djust be in the urinary tract, thats probably what your doc meant. something similar happened to me, i had one that was untreated for a long time, and when i finally got antibiotics, the bacteria went away, but i still have symptoms even almost a year later. my urogynecologists think it's interstitial cystitis, which is an irritation of the bladder lining with no infection present. do some research on that. i take a bunch of pills, but theres really no cure, im going to start physical therapy for it too.
as far as i know it has nothing to do with bcps.