My guinea pig is breathing funny?

I have a feeling you are not taking her to an exotic vet, they know so very much more about guinea pigs then a standard vet, I strongly suggest you take her to an exotic vet. Yes she has all the symptoms of an upper respiratory infection, not including pneumonia. She might need a different antibiotic, guinea pigs can only take 4 antibiotics and finding the one that will kill the bacteria they have can be a bit difficult. When y little Hoshi had an URI it took him 8 wees on meds to totally bet it, some URI'S can be quite a challenge for guinea pigs. Believe it or not I found Carefresh bedding to be very dusty and was what caused Hoshi's URI to not heal, as soon as i put him on pine bedding he healed quickly!!