[umpjim]

The batter got back in quickly and there was a delay in the pitcher's reaction so the ump might have not connected the two actions. With a R3 I always suspect shennagins from the batter and would have had a no pitch per this rule comment from MLB.com:

"Rule 6.02(b) Comment: The batter leaves the batter’s box at the risk of having a strike delivered and called, unless he requests the umpire to call “Time.” The batter is not at liberty to step in and out of the batter’s box at will.
Once a batter has taken his position in the batter’s box, he shall not be permitted to step out of the batter’s box in order to use the resin or the pine tar rag, unless there is a delay in the game action or, in the judgment of the umpires, weather conditions warrant an exception.
Umpires will not call “Time” at the request of the batter or any member of his team once the pitcher has started his windup or has come to a set position even though the batter claims “dust in his eyes,” “steamed glasses,” “didn’t get the sign” or for any other cause.
Umpires may grant a hitter’s request for “Time” once he is in the batter’s box, but the umpire should eliminate hitters walking out of the batter’s box without reason. If umpires are not lenient, batters will understand that they are in the batter’s box and they must remain there until the ball is pitched. See Rule 6.02(d).
The following two paragraphs are additional material for Rule 6.02(b) Comment, for Major League play only:
If pitcher delays once the batter is in his box and the umpire feels that the delay is not justified he may allow the batter to step out of the box momentarily.
If after the pitcher starts his windup or comes to a “set position” with a runner on, he does not go through with his pitch because the batter has stepped out of the box, it shall not be called a balk. Both the pitcher and batter have violated a rule and the umpire shall call time and both the batter and pitcher start over from “scratch.”
Rule 6.02
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The following paragraph is additional material for Rule 6.02(b) Comment, for National Association play (in lieu of the additional two paragraphs, above, that apply to Major League play):
If after the pitcher starts his windup or comes to a “set position” with a runner on, he does not go through with his pitch because the batter has stepped out of the box, the umpire shall not call a balk. The umpire shall call an automatic strike if Rule 6.02(d)(1) calls for such sanction."

Thers's also the "any action designed to cause a balk" rule but this post is already too long.