It's possible that there is a secondary infection to the URI and the current medication isn't treating the infection. It initially helps with the symptoms, but then it's effectiveness wears off. I would ask the vet to do a culture and sensitivity test of the nasal passage or throat (or eye), wherever there's discharge. This will tell the vet exactly what type of infection you're dealing with and the sensitivity test will show exactly what med will treat it.
With my girl who's very prone to URI due to herpes, we've found that drops in the nasal cavity helps clear up the linger infection causing the sneezes. The last time she had medication, we were giving her Zenequin (antibiotic) and nasal drops. We continued the drops until the bottle was empty and I think it helped clear up her bacterial infection to just a trace, which is excellent and she's been sneeze-free, with no snot slinging or sniffling for about 2 months.
Have they been tested for herpes using the Idexx Real PCR URD test? That could be something else to figure into the equation. If they do have herpes, that suppresses the immune system and it makes recovery time a bit longer than normal. Also, if they have herpes, there's no cure for it, but it can be managed very well. Switching to a grain free diet will help as well as adding lysine to their diet.
If your vet isn't willing to dig further to find out why this is continuing, I'd look around for a different vet and get a second opinion. Or, you may need to do your research here and other places online and ask for certain tests and treatment options. I'd highly recommend finding a cat only doctor if there's one in your area and getting a second opinion.