You doctor's reasoning is perfectly valid, but resistance is unlikely taking the two together.
A Herxheimer reaction can start nearly as soon as you start the abx. Mine, which just took the form of a fluey feeling and an incredibly runny nose, started the day after. I also felt very sleepy: in fact I slept a lot of the day for the first couple of weeks. Everyone is different though, probably because everyone's lesions are in different places.
Keep us informed, and the very best wishes,