Could it be that the bacteria he's getting is resistant to the antibiotics used? Has he had a culture done of his urine to determine what the bacteria is and what it will respond to?
I had a couple UTIs during my last pregnancy (when I'm more vulnerable to them anyway). The second one was likely just a continuation of the first; the first antibiotic beat it back but didn't get rid of it altogether. When I had the second one, my midwife sent my urine for a culture and prescribed a stronger antibiotic.
The alleged UTI/foreskin link has been thoroughly discredited. Circing your son won't guarantee he will never get another infection. Here's more info on that just in case anyone brings it up:
http://www.nocirc.org/statements/breastfeeding.php (see the sidebar).
Nor should you retract him for cleaning. That is totally against the recommendation of the AAP and will only introduce pathogens into the area, not to mention cause bleeding, pain, and scarring that could lead to the need for a circumcision later on in life. The foreskin shouldn't be retracted for cleaning in infancy - the only person to retract the foreskin should be the child himself when he is ready.
I would definitely ask for a urine culture and I would also get vitamin C in the form of sodium ascorbate and cranberry extract into him. You could either see if he will drink some cranberry juice or get the cranberry extract capsules, open them up, and stir the powder into some applesauce or yogurt or something. Blueberries are also excellent for combatting UTIs, and very palatable to young kids - I buy frozen blueberries and defrost them for my son.
Good luck, and make sure any doctors you consult don't either a) blame his foreskin for the problem or b) tell you to retract it or cut it off! If they do, find another doctor as they are obviously ignorant.