An interesting tidbit I saw on ESPN's College Football Live today. John Saunders, Doug Flutie, and Trevor Matich went to the demonstration field in the studio to discuss primarily the Wildcat (Wild Hog, Wild Reb, etc.) formation. Though Michigan has run out of this formation very few times this year, the emphasis of their segment was on how running out of the shotgun formation is particularly taxing on the center.
Perhaps not coincidentally, Michigan's offensive line (especialy David Molk, the center), has been very good in pass protection, but has struggled when running the ball out of the shotgun. Matich's demonstration on why running the ball from the Wildcat formation is difficult may explain why Molk has struggled.
The general premise of the bit was that the center snapping into the shotgun for a pass play (or, theoretically a draw) can simply snap the ball and take steps back to protect the passer. For a run play, however, he must snap the ball, turn to block the defender in his area, and fire forward, all at the same time. In Matich's demonstration, he illustrated how the center was going to be prone to bad snaps from this formation, because he is turning his hips to the defender and firing forward before the ball leaves his hand.
David Molk hasn't had many bad snaps this year (despite playing in poor weather in the Notre Dame game), but he has had trouble blocking against the run. Is it possible that he has focused on making sure the snap gets to the quarterback, at the expense of turning and firing forward? I would assume that the shotgun snap is emphasized by the coaches in practice, and perhaps that is at least a partial explanation for Molk's issues in run-blocking.