At FiveThirtyEight.com Nate Silver says that the results being reported for the recount are now not indicative of what is really happening in the race. The number of challenges has accelerated dramatically in the last couple of days. The number of challenges is already around 2000 and could top 3000 ballots when the recount is over. The problem is that the challenged votes are reported as "other" and there is no way of knowing how many are frivolous and will be rejected. This is why the recount shows both candidates have lost hundreds of votes in the recount. Everyone seems to agree that a large portion of the challenges will be rejected but the key is how many of these challenges represent clear votes for Franken or Coleman that were challenged by the other side and how many are for votes that were ruled not to be votes for either candidate and were challenged.
Nate is a pretty smart guy so I take what he says as an indication that we really do not know who is going to win at this point.
http://www.fivethirtyeight.com/2008/11/amid-epidemic-of-challenges-coleman.html