Here is a pretty good interview with a very experienced herp vet. He goes into detail about respiratory infection in Ball Pythons.

http://www.blogtalkradio.com/reptile...ile-veterinary

In which he states you will typically notice improvements after the first three to four injections. You have not mentioned how long of an antibiotic regimen your vet has given the snake. Even with the right antibiotic, if you don't give it for long enough, it would still be ineffective.

I would think the next step would be to do a culture and sensitivity test on a sample of mucus taken from a tracheal swab. From there your vet will give you whichever antibiotic works best against that particular pathogen.