No, they only include the votes cast on Nov 2. I believe the state must count provisionals but not absentees unless requested.
http://www.cnn.com/ELECTION/2004/pages/results/states/WI/P/00/index.html
Force the issue through the Kerry / Edwards "count every vote" theme. And while you are at it, keep score of the uncounted absentee ballot tally. Then there will be a number to use in '08 for how many military absentee voters were disenfranchised.