First off, while I think every vote should count, there still seems to be one super critical fact missing from both this story and the coverage on the linked web page for the people doing the count: Did the failure to count those ballots change the outcome of the vote? This is super critical because if it did, the wrong person is in office, and whether or not he or she is a member of my party, does not belong there. Absent that, the issue drops from super critical to serious. It is serious because it needs to be fixed for the next election, but having not affected the outcome of this election, is moot to the purposes of governing.
Next, for all you idiots who think Deibold/Premiere has morons doing their programming work and don't see the need for a technological assistance in vote counting, counting is easy if everything that needs to be counted all comes in the same form and arrives at the same time. Real elections don't work that way. Handling how to deal with adding and removing ballot sets strikes even me, as a non-programmer, as a task that requires a good bit more insight than even a proficient college grad would have. As for those of you advocating not using machines and or computers to tally millions of ballots in 24 hours: please, go back to your caves and don't come back out until you have at least mastered the concepts of 'fire' and 'the wheel.'