I could be wrong about this, but it seems to me that with one exception (the 2001 championship game), the team that's won in the playoff games between these two has been the one that wasn't favored to win. In 1999, the Sioux were expected to win it all, but BC upset UND in the NCAA regionals. In 2000 during what was supposed to be a rebuilding year for UND and a year in which BC had no fewer than three Hobey finalists, the Sioux won.
I remember the Eagles being the favorite in the 2001 championship game because they were once again loaded with talent. BC won that game in OT after a patented Blais comebak. In 2005, UND wasn't supposed to surivive the East Regional against either BU or BC. The Sioux steamrolled both of them. Last season, I thought the Sioux had the momentum heading into the the Frozen Four, but BC came out hard and knocked UND off its game. The Sioux never recovered after falling behind 3-0.
This year, BC is the team on the hot streak and the favorite to win it all. I'm hoping that bodes well for the Sioux.