From the article, it appears only this one problem has turned up. The article is mainly about the Pottawattamie County, Iowa county problem where an ES&S programmer failed to account for ballot rotation when programming their machines. But it also discusses other problems this one problem turned up (the Logic and Accuracy test should have revealed the programming error - why didn't it?)
http://votetrustusa.org/index.php?option=com_content&task=view&id=1378&Itemid=51(this is near the end of the article)
Krogmeier also told me that there was a problem in Dallas Co., a suburban county just to the south of Des Moines, where a professor from Drake University asked to use the AutoMark machine when he voted. He went through the ballot, marking his choices, and when he was through he checked the ballot to find that one race had been swapped. His ballot was "wasted" and he voted again with the same results. He then agreed to allow a poll worker to sit and watch while he voted. The same thing happened and the machine was taken out of service at that point. The problem was the same as in Pottawattamie County except that we only know of one ballot that was affected. How many more were marked incorrectly on this and the AutoMark systems used in 20 other Iowa counties.
Ballot programming errors are a new threat at every new election, and it is time election officials realized it. Problems are cropping up all over the country, and there is no indication that they will abate. Elections officials cannot just accept that what they get from ES&S, Diebold, or any other vendor is 'good to go'. They must test the software and they must be heard when there are problems with it. If it hadn't been for an observant county clerk in Pottawattamie County, the machines' choices for County Board of Supervisors not the voters' choices would have been declared the winners.
Either the vendor does the programming, or the county does it. The vendors want to do that work because they make a lot of money for the service. ES&S requires that they do the programming for the AutoMark machines in many of their contracts. Counties could do the work themselves but the cost of the programming software is so expensive that it is hard for some counties to justify the expense.