Update 11/10/13 - This issue has been resolved with the release of the November 2013 Cumulative Update. You can get more information here.
With the release of the September 2013 Cumulative Update for the Lync 2013 client, there is a known issue with presence not updating based on the user's free/busy status from their Exchange calendar. You can find more information about the issue in KB2883716. This issue will be fixed in a future update.