I was watching the Miami-Syracuse game this afternoon, and was very confused with the penalties at the line. Sometimes a flag was thrown and the play was negated, other times a flag was thrown and the play stood. Every once in a while, there was a whistle to kill the play before the snap. Could someone explain to me the different NCAA NZ infractions, the penalties, and when the ball becomes dead?

Since this is an NCAA game, the basic idea is this.
NZ fouls by the offense are Dead Ball fouls, i.e. the flag shuts the play down before with the snap.
Defensive NZ fouls may or may not be dead ball fouls, therefore the offense can choose between a five yard penalty and "replay" the down or take the results of the play.

Here is one way to think of the difference between dead ball fouls and live ball fouls. If, as in the case of an illegal shift or motion a delay in the snap could have prevented the foul, it's a live ball foul. The flag is thrown and play continues. If the foul is committed and could not have been negated by a delayed snap, it's a dead ball foul and play is stopped and the foul administered.

In all three books (NFL, NCAA, FED) if the offense commits an NZ violation, it's a dead ball foul, no play. In NFL and NCAA, if the defense jumps offside, it's a live ball foul. If a defensive player touches an offensive player, or causes the "O" lineman to move, then it's a dead ball foul for encroachment. In FED, there is no offside foul, all NZ violations are dead ball fouls (encroachment).

Bob