If your subtitles are not correctly coming up at the correct time, this is usually due to choosing "Line by Line (1 Line)". 

With this choice, their is a character limit per line, so if your subtitles expand this character limit, they will overlap into the next line and will make the subtitles out of order with your voice narration. 

We recommend that you limit your subtitles per timestamp in this choice by 60 characters to fix any issues you are experiencing.