I've never bought "Republican-biased voting machines" conspiracy theories. However, I can see the possibility of programming errors which, in ambiguous situations, might allow a vote to go to the first candidate listed on the ballot, regardless of party affiliation.

In Florida, the order of candidate appearance on general election ballots is determined by the party affiliation of the current Governor. Since the Governor at the time of the 2006 election, Jeb Bush, is a Republican, the names of Republican candidates appeared first in all partisan contests. So, if there were to be a programming error it would likely equate to a Republican bias. If unresolved, it may become a Democratic bias at some time in the future, in which case we'll likely hear Republicans taking their turn doing the complaining.

It needs to be investigated, and Republicans need to understand that stonewalling is, ultimately, counterproductive to their own interests.