Its not uncommon for one antibiotic to not work for an URI. I recently had a lesser get an URI. We did 3 weeks of baytril with no luck. We ended up switching to fortaz and within 2 weeks she had mass improvements. I also did a nebulizer daily with chest rub and eucalyptus oil.
Most vets do not know how to treat URI so a bit of knowledge on your end will help in the future.
On a side note has anyone had to use an antibiotic other than baytril or fortaz for an URI?