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Some of the ways the absentee vote system can break down:
Ballots can be lost or damaged in the mail.
Ballots can be ignored. In Florida's Broward County, investigators who had heard stories of widespread negligence in the elections office found 268 uncounted absentee ballots from a September 2002 primary in the back of a file drawer.
In Florida and most other places, absentee ballots are machine-readable optical scan ballots. Stray marks, food stains, odd colored inks or other problems can prevent ballots from being read properly by the automated system.
When ballots require manual interpretation, that "opens the door to subjective judgment, and canvassing boards have been known to be biased," Jones says.
Absentee voters miss out on the chance to correct errors such as voting for two competing candidates. When optical scan machines are used at the polling place, such problems can be detected, allowing the voter to complete a new ballot.
In Florida particularly, there's a long history of absentee votes being discarded or manipulated. Hacking the absentee vote can be decidedly low-tech.
The Miami Herald won a Pulitzer Prize for showing how fraudulent absentee votes swung a 1997 mayoral election in Miami. In one of the most colorful scams, campaign workers armed with boxes of absentee ballots paid homeless citizens $10 a vote to support their candidate.
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http://www.eweek.com/article2/0,1895,1640826,00.asp
(While I disagree with this article's completely negative tone regarding paper, it has many good points regarding the problems with absentee balloting)