As far as I can see, the issue is this: the Fed is trying to apply a macroeconomic loosening of the money supply to fight the deflation from the financial crisis. For political reasons, the old school Keynesian method of borrowing for more government spending can't be used. So, they are maintaining low rates to try to jumpstart the economy. Unfortunately, this money has to enter the economy through a financial system which is geographically imbalanced. So, we get inflation in SF, and NY, less inflation in cities with less finance industry, and deflation in much of the rest of the country. This seems to be the big economic issue of our time in the developed world.
Why we have two economies, and the financial system isn't arbitraging this difference away, I'm not sure. I recall reading an economist (Harold Innis maybe?) who warned about the centralizing effects of a Keynesian inflationary theory. Anyone know more about this?