I wouldn't be all that worried, this is somewhat a predictable problem. With upper respiratory infections a culture and sensitivity should be done to use the proper antibiotics. Essentially, this is collecting a sample of material from the nares, trachea, and/or the lungs (if pneumonia) to grow the pathogens that are present. Then these colonies are suscepted to multiple antibiotics to see which one will prove to be most effective.
This step is often skipped for one of two reasons... the veterinarian's lack of confidence in collecting the samples, or it is a cost consideration. Both are poor excuses because the sample is easy to obtain when experienced and it doesn't cost that much (about $40-60 here, probably much cheaper in the US) Baytril is often used in reptiles as a "cure all" because it is mighty affective against most pathogens present. It was only a matter of time before a strain was resistent or became resistant.
In poor doing animals, often an antibiotic is began while the lab work is being done (several days). This gives a head start in hopes that the correct antibiotic was chosen, and if not, then the medication is switched when results are in.
Of course other reasons that treatment fails happen when the snake is otherwise immunocompromised from poor husbandry, a viral infection, or other complicating factors.
Ian