As far as I know First has used the same match scheduling algorithm since 2008. The software is simply called MatchMaker and was produced by Idle Loop Software. It was first used I think (correct me if I'm wrong) in 2007, and was later modified in 2008 after the scheduling issues discovered at the 2007 regionals. Since 2008 I don't believe it has changed at all, so what you are seeing are just flukes in the software, when it tries to balance the alliances Red/Blue.
You can find more detailed information on how the algorithm works
here (
http://www.idleloop.com/matchmaker/ ). I know from experience that the algorithm generally creates generally fair matches, but don't forget that the software receives no information about the team other that the team number. It does not know the record of any team, or if they have a "good" robot this year. (Or any year)
Edit: Looks like someone beat me to it... What also might be happening, is the large increase in rookie and #3000+ teams, and that is messing with the "balancing" of alliances. Thoughts?