I would ask your vet to do a skin scraping of that specific area. She could have a staph intermedius (pyoderma) that's coming forth, but it likely would have spread by now. Did her itching increase when the pollens shot up w/ spring?
If your vet is not the best w/ skin issues, I'd def recommend seeing a Vet Derm - they're more $, but extremely effective in the long run.
This link on approaching allergies may help too:
http://www.yorkietalk.com/forums/die...tart-here.html