Baytril is not always effective against RI's. Also, whatever bacteria/virus is the cause of the RI, they are constantly evolving to find a way around/through whatever is being used to combat them, and Baytril has been around a while. I had a very interesting talk with my dog's vet in regards to Frontline and how it doesn't seem nearly as effective now as it did 10-15 years ago. Different scenario, same general theory at work.

Secondly, it may not be a bad idea to be seeking a new vet. I know you don't want to come off like you don't trust yours, but it seems that way...and that can put you and your vet in an incredibly awkward experience. A trusting relationship with your vet is as important as your vet actually knowing what they're doing, IMO.