Hey JDOM,
I have had the same issue in a couple leagues in the past. MFN follows the tiebreaking procedures of the NFL. The link is below.
I am curious to see if this follows suit. There have been 2-3 times in which there was a bug and the team not winning the tie-break was the one selected for the playoffs. JDB said he was going to fix it with the new release, which I believe has been done. If you follow the tie-break rules and it seems wrong, send JDB a pm to inform him.
NFL tiebreak rules:
http://www.nfl.com/standings/tiebreakingprocedures