Welcome to the world of buns with respiratory issues.
Has he been on any other Abx?
I personally would ask the vet to perform a C&S Swab of Buckley, to see what kind of infection it was. That way, they can deem which ABx the bacteria is susceptible to.
If it makes you feel any better, Ginger's been on ABx for ~two thirds of her entire life so far. We've had Baytril, Septrin, Depocillin and now i fear, we'll be changing over to Zithromax as advised by Richard Saunders, of Langford Vets, one of
THE rabbit vets in the UK.
She's also on daily metacam - it might be worth asking your vet if metacam is an option, as its an anti-inflammatory, which may help.