If ANYTHING comes in with scaley ANYTHING, I first think mites and diet. If she is eating what she is supposed to be eating, then it's not a diet issue. I would think it is a sarcoptic or demodex mite issue. They usually manifest themselves on the head and ear ridges, causing scaling, itchiness, etc. It may take a few deep skin scraping to turn anything up, but once you do(or don't, I'd treat it anyway by what it looks like) you know what you are dealing with.

She could also have a fungal infection if she was being kept crowded and dirty for a long period of time. Especially since that is how she came in...

I would take both to a vet and either get them a paramite dip once per week for 2-3 weeks or a few ivermectin injections. Whatever the vet thinks is necessary. You don't want that spreading to any of your other furry critters.