I've seen this episode many times, and I finally spotted a 'goof.'
When Kay Freestone and Walter are in the projection booth, and she sends him to get more films, she changes the counter to read '241.' Walter says to her, "There's a change over coming up in about two minutes." She volunteers to make the change while he goes and gets the film.
Obviously we know she goes and kills McAndrews. My confusion is that her tape recorder says, "You have 4 minutes." Now she takes every last second of that 4 minutes to get back to the booth and make the change over.
BUT - The counter signaled a change over is just over TWO minutes. I'm sure you can see the dilema here.
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?