Hello,
I'm a new kitten owner, and one of my kittens recently had a health scare, where I learned a little more about the herpes virus.
My 4-month old kitten at the time was feeling extremely feverish and lethargic. He's usually running around, causing mischief, but he was so uncharacteristically sluggish that I had to take him to the emergency vet hospital that same night. The vet took his temperature, and it was 105.6 degrees (normally should be around 102-103). After waiting there for two hours for his blood test, everything came back negative, (similarly, urinalysis came back negative as well) and my vet then told me that he suspected that my kitten had the herpes virus.
He explained that shelter cats in general are very likely to have the herpes virus, since it is viral and can be transferred pretty easily from cat to cat. Just like in humans, herpes in kittens remains latent until some sort of stress to the kitten (new environments, new animals, etc.) causes the kitten to have a decreased immune system, which is then when the kitten will have a herpes flare-up and have similar symptoms as any other viral infection (e.g. fever, lethargy) and likely with symptoms affecting the eye (e.g. frequent squinting, yellow/brown discharge).
The worst part was that, when I asked why he thinks it's the herpes virus, he responded that he actually can't say for certain, because apparently there isn't any definitive test for herpes. The only way they can know is by deductive reasoning and eliminating all other likely diagnoses.
I hope that the scant insight I have helped you a little bit. When you get the opportunity, you should ask your vet how he/she knows that your cat has herpes if the medication doesn't seem to work. From what my vet told me, it does seem like the adoption process might have stressed your kitten out a little bit, thus causing a herpes flare-up that was untreated. Although, I'm a little skeptical because of the fact that there is no definitive test for herpes, so it may be possible that it's not herpes at all. Please update about how your kitty is doing after you've given her the medication.