Timeline not in sync with Audio

I thought I saw a post on this recently, but I can't find it. I have a timeline that should pause at a cue point. I need to set the cue point at least 3 seconds after the audio stops for it to work. I noticed everything on the timeline is out of sync. This is a .story file that was published over 3 years ago I'm updating with some new audio in other slides. 

 

Has anyone else having this issue or do I need to put a case in for this?