A few times since switching to 2.4 (on Windows XP box) I've seen the same team kick off to start both halves of a game. It seems to be a fairly random occurrence (rerun with the same teams/books and kickoffs are normal), but it's definitely happened now in at least two games I've run in the WFL, and in a game the first week of the current SPMFBL season run by another coach as well.
I think the problem is with the initial kickoff. This past weekend I was running a WFL game with serious playoff implications and therefore taking copious notes. I wrote down "langs win toss/receive" and then have a long list of events until the first team scored, which should have been the Langoliers by my possession notes but was actually the Eagles. Pausing the game and quickly checking player names I'd jotted down against the league database showed the Langoliers kicked off rather than receiving (which the transcript after the game confirmed) so all my notes needed to have the team names reversed. The Langoliers then kicked off to start the second half as well. It's always possible that I wrote down who won the toss incorrectly, but I was trying to be pretty careful....I can supply the transcripts of the two games that this happened in this week (one WFL, one SPMFBL) though I'm not sure they would be helpful.