Batter's position in box

[bob jenkins]

If the batter starts partially (or entirely) outside the box -- fix it if you can. If you don't fix it, then there's no penalty for this action.

The penalty is only for hitting the ball with the foot entirely outside the box (or, in some codes, touching the plate). The batter didn't do that in your play, and so "no call" (well, just the strike) was the right call.

[MD Longhorn]

A) Don't let them go ape-sh&%. Even if you botch a call, like it sounds like you did. They still don't get to go ape-sh&%.
B) The "penalty" for not being in the box is nothing... it's basically - don't allow a pitch until he's in the box. If he got in and slid out before you could stop the pitch, it's just a pitch. Not an out.
C) The penalty for hitting the ball while touching the front line is also nothing.

All you have here is a foul tip.