Do you know the strength of the baytril used? There are different variations and if he made it up (as my vet does) -- hopefully he gave you the right dose for their weight. 5 days is way too short of a time for the meds to work fully. Chances are your rat will get sick within a month with the same thing. It should be 14 days at the very least. My vet always doses for 14-21 days (depending on the problem). If he is going to give you a problem about the amount of days. You can check out
Ratguide to do some research on the matter - you can printout your findings and take them to your vet to see. Some vets really don't know what is up with rats and what they should be doing. They dont' get enough to see in their practice, and sometimes it seems more like a trial and error with some of them. Fortunately I've found an awesome vet who is reasonably priced - He admits he doesnt know everything about rats, but he is open to my suggestions and findings.
Good Luck with that - please get a second opinion if you can't get your vet to increase the treatment time. Also double check the times you need to give them to your rats. This may not apply to you, but usually baytril is given 2x's a day (at least with the medical probs I've encountered here at my rescue). ** I wouldn't split up the .3 dose though, so please do not do anything like that until you've consulted with a vet**