Essentially, it is a batter's responsibility to be in stance when the bowler starts his run up. If not, he will get a warning, and potentially a penalty.
See wikipedia on fair play:
In normal circumstances the striker should always be ready to take strike when the bowler is ready to start his run up. If he wastes time, in the first instance the batsman is warned by the umpire. That warning applies to the batting team as a whole and each incoming batsman is informed of that warning. If there is further time wasting by any batsman in that innings, the umpires award the fielding side 5 runs and inform the Governing Body so it may consider further disciplinary action.
