I know this is an old thread, but I figured I'd add to it so I can help someone out somewhere, if they decide to read it later. You've been given some great information; I just wanted to add to it.
Upper Respiratory Infections, like hhmoore said, are almost always caused by husbandry issues, and most often simply by too low of temps. Baytril/Enrofloxacin is an antibiotic that is commonly used in reptiles, though it is not always the safest. Baytril has not only been known wipe out intestinal flora (like Kaiyudsai said), but can also cause necrosis at injection sites (which is a far worse problem than a URI/scale issues). If you do get Baytril, you have to make sure you varying up where you are injecting it to prevent this, and it is also important that you are making sure you're getting it intramuscularly (in the muscle) and not subcutaneously (under the skin/scales).
Because of these risks, like Tim said, vets more commonly use Fortaz/Ceftazidime anymore over Baytril/Enroflaxacin. I like Fortaz MUCH better; it is much safer to use, and is done every 72 hours, not daily.
However, as was also recommended above, you will never know what kid of bacteria you have without doing a culture, which most vets will recommend. This is costly and not always practical for most people, but it will tell you what kind a bacteria is causing your snake's URI (ie Pseudemonas, or Staph, or Strep), and what medications it is resistant and sensitive to. A bacteria may be easily killed by a certain drug (sensitive), or may have a shell/fighting enzyme/defense mechanisms that make it unaffected by a certain antibiotics (resistant). So if your bacteria that is causing your problem is resistant to your drug, it won't show any improvement - or if it does, it will only be for brief period of time before it returns. Most people make the mistake of thinking they need a "stronger" medication, but in reality it's not a strength that matters - you just need the correct one for that specific bacteria. Your snake could be resistant to Baytril and may never get better with it, because your snake's bacteria is resistant to it.
All in all, see a vet, run a culture, have them pick the most applicable mediation/antibiotic for your reptile, and fix your husbandry. Hope this helps. Cheers!