According to this blogger who is onsite observing the recount, these problems have arisen form improper marking on the ballots. Some wards missed hundreds of votes because of they used the wrong type of ink. He also said that ALL the memory cards for the Diebold machines have gone missing. There are attorneys onsite observing as well.
http://www.bradblog.com/?p=5568
This was my guess before I got down to read your post. The conspiracy, black helicopter, the polls are wrong Ron Paul supporters are always looking for something in the shadows.
The same with the Algore supporters that couldn't vote properly (and in my view most should be voting anyway) then blaming the system. The hanging chad folks. Look you f'ing idiot if you can't punch a piece of paper out of a ballot I don't think you should be voting. If you can't fill in a bubble or complete the arrow (my ballots) than just do the patriotic thing and let competent people do the voting.