My son who is 22 had an infection in his ball sac.  He was on antibotics twice and is still having pain.  He went to his PCP and he said it may just take some time to get over and to take aleve for the pain, and he will recheck in two weeks.  I am concerned, but something serious be going on?
I presume the infection is in the testes and not limited to skin of the "ball sac" as you call it. If so the common causes are spread of infection from the urinary tract or occasionally affection from mumps among other causes. My practice would be to do an ultrasound of the urinary tract as a minimum to make sure there are no abnormalities there. Your physician is right in saying that it takes some time for the infection and pain to resolve after giving proper antibiotics for proper duration. Occasionally it might take 3 months for the swelling and pain to settle completely.