Honestly, Joe's answer is a bit bizarre. Any good appraiser should be limiting comps to the same city---my house is in Sophie's zip code, for instance, but it's in Oakland, so I would fully expect it to appraise at a fraction of her value. Because guess what? I paid a fraction of what she paid, and I don't have access to the same schools, parks, and services. You can bet no bank would refinance an Oakland home in 94611 based on a series of comps from Piedmont; the same should be true in reverse. This isn't a matter of maps; it's a matter of basic competence on the appraiser's part, since Piedmont is certainly not the only city where school quality drives housing cost.
This is an old post so I imagine it's long since been resolved, but the solution is, unfortunately, to start the process over again with a new lender and new appraiser and hope for better luck.