I've always done my bottles with plain hot water between feedings, soap and water before using bottles for a set of calves the first time. But then my calves come from the same location and I haven't had problems. Picked up a load of calves from a different dairy week-before-last and I did disinfect all bottles with hot water, soap, and then soaked in chlorhexidine solution before I used them for the first time (since then I've just been rinsing with hot water and no problems with any calves).
My bet's on the calf still having the same problem he had before - you just didn't give enough antibiotic or for long enough to kill the bug completely, and it's showing up again now.