I've heard claims that those votes aren't counted, but I find that awfully hard to believe. The presidential race is not the only race on the ballot. Those absentee voters are also casting votes for Senator, state legislature, school board, mayor, referendums, etc. Many of those races will be determined by the absentee votes, even if the presidential election isn't. It may take them time, but I'm fairly certain all those votes are eventually tabulated. Do you have a link indicating they are not counted?
Back during the recount fiasco, I remember that the California vote total did not change from November 4 through November 30, indicating that no absentee ballots were added. Those links are no longer available, as they have been replaced by the official state total given around Dec. 15, 2000. However, I did find this link from MSNBC which contradicts my earlier claim: http://www.msnbc.com/d/d2k/g/state_CA.htm This gives an unofficial count on election day of 9.3 million votes cast for either Bush or Gore. The official State tally given out six weeks later totaled 10.4 million votes for either Bush or Gore. This would correlate with the 1.1 million figure given in another site for the number of absentee ballots cast, indicating that the absentee votes were indeed included with the Dec. 15th certification.
http://www.ss.ca.gov/elections/sov/2000_general/pres.pdf
Please note that this is an addition of 1.1 million votes that were not included during the immediate aftermath of the election when the cries of "Gore won the popular vote" were loudest. I am willing to concede that my earlier claim was in error. However, I am not willing to concede that Gore won the popular vote since there is no certainty whatsoever as to what the actual popular vote was in all 50 states, nor is such a tally even relevant.
I find it highly ironic that the Democrats would even concern themselves in the popular vote tally considering that in the entire history of the Democrat Party, only five Democrats have ever managed to capture a majority of the popular vote in any presidential election.