Kelly, I have no idea what it could be, but I do think that the reason they want to keep her in is because they don't have much time and want to squeeze it in in between consultations. Vets do that a lot. I know they sometimes do skin scrapes on dogs to check for mites, but if the vet has already ruled out mites I have no idea what they are doing! I hate to say it, but if I was you I'd travel a bit further and go to a different vet. I know its a bit of a pain, but it is what I would do.
Whatever happens Kelly, I am thinking of you and your piggies. I hope it gets sorted out quickly.