Larger towns or reporting units tend to machine count their votes. The smallest ones tend to hand count. There is a middle range of reporting unit size in which both methods are used. If we use only the reporting units larger than the smallest machine-counter and smaller than the largest hand-counter (in other words, the mid-range in which both methods are used), we find that Obama won 63% of contests if votes were hand-counted, and only 39% if votes were machine-counted.
In the above graph, the data points below the mid-line show contests won by Obama, while the data points above the line show constests won by Clinton. The blue circles are hand-counted totals, and the red crosses are machine-counted totals. As the numbers above suggest, there is more blue below the line, and more red above, especially in the mid-range of vote totals.
This analysis eliminates the size of the reporting unit as a factor in the vote totals difference. The main factor seems to be the method of counting votes. Hand counting favours Obama, machine counting favours Clinton. It is quite clear. It isn't that people in different sorts of places vote differently. It is that people in different places use different methods of vote counting.
I have a few more ideas to tease out the method they used in greater detail. I'll keep you posted.