I have read Palast's stuff on Florida before. While on the surface this reads like the allegations of police blockades in black neighborhoods and few-and-far-between incidents of problems with individual election workers, it's a different tale altogether.
Palast focuses on the scrubbing from the Florida voter rolls the names of alleged felons, and the way that the job was monumentally botched, revoking the right to vote for criminals who had a legal right to vote. He makes great hay out of the fact that the company that screwed things up -- a division of ChoicePoint, founded by a Republican donor, now deceased -- was located in (cue scary music!) Texas. He also makes the accusation that Katherine Harris violated the Florida law by making those who were mistakenly scrubbed reapply to vote. Most of the non-felonious criminals were black, and there were supposedly more mistakenly scrubbed than made up the winning margin for Bush, so, the thinking is hundreds of potential Gore voters weren't allowed to choose him by Harris and Jeb Bush.
Essentially, Palast argues that ChoicePoint's ineptitude was too beneficial to the Bushes to be an accident. As someone who once was in a board meeting that was entirely about ChoicePoint's inability to get my department necessary applicant information, I can tell you all that I am not surprised, and don't think it was a plot.
When reading Palast's story at face value, complete with charging after Fla. officials through parking lots and being rebuffed, it seems like a damning argument, but the question is, why is it that the actual alleged victims of what went on don't embrace Palast, and continue to hold on to the butterfly ballot and the bogus charges of racism as the cause of the "disinfranchisement?" I hate to say I won't believe it until I see it in the mainstream media, but I don't think it would allow this story to languish in the pages of Harper's a year and a half after the fact if it could stand up to scrutiny.
You have a good point about the mainstream not picking this up. Other than that I don't know any counter-arguments.