I never got the impression that Walter actually noticed the cue blips. I always thought that Walter just commented on the depraved state of entertainment and how he saw a man blow his brains out right after he returned to the projection booth. When Columbo noticed that the suicide scene had a cue blip preceding it, that meant that Walter was lied to about the timing of the reel change, i.e. that it was much later than Kay had told him, giving her opportunity to commit the murder.
Plus, there was no nickel on the floor proving that....whoops. I’m getting my episodes mixed up, lol.