Never thought much about it but, from your description, it sounds like:
She set the timer ahead, so that Walter would think (and could tell the cops later) that she only had 2 minutes (not enbough time to commit the murder and come back); but really, she had 4 minutes.
That's assuming she re-set the timer before Walter looked at it (to fool him, and to help her alibi). But I don't remember. Does that make sense?