Hi!
Any course should take about 3 weeks (4 weeks on septrin/sulfatrim/bactrim). It can take time for the symptoms to come down.
See your vet promptly if the symptoms have not come down within a week, are getting worse or are coming down soon after you have stopped the antibiotic.
As your vet has already eliminated stones, you are in this case likely dealing with a sterile interstitial cystitis (IC) which at the moment cannot be healed as we don't know what is causing it. It is become more common in the last decade. Thankfully it is eventually going away on its own, is not life shortening and is not causing any bladder stones. If that is the case, please contact us for more info. Right now, your vet is doing exactly what they should and giving you the correct medication.