Medication's take time to build up in the system and begin working so that may be a factor. What med was prescribed? If it's clavomox you may want to discuss switching. :-). You can also run a test to see of your pup is actually resistant to that type of medication. If it's JUST a cough without other signs of URI have the throat and chest area's been checked for problems yet? Generally you don't want to suppress a cough in our pups but if time and severity indicate it your vet may prescribe hydrocodone at the appropriate time. Just keep talking to them about your concerns. If they are resistant to your participation you can always consult another vet like said. Hope your pup is feeling better soon.
I'd call the vet you got the medicine from and see if he wants to change medicine. If you are not satisfied with his treatment, I'd suggest you take her to another vet for a second opinion. Best wishes.