When I first heard about this, I thought it was an internet joke. Patron saint of disputed elections.
Some people claim it is due to demographic factors.
The data at least suggest it is not due to whom the county voted for. The graph has boxplots for the percentage of undervotes in the counties, broken into groups depending on who the county went for and what type of voting method they used. The vertical axis gives the percentages of undervotes. What you see is that whether the counties went for Bush or Gore, those with optical scanners tended to have many fewer undervotes than those with punch cards. I don't know why, but they are sort of small counties, Washington and Columbia.