Storyline Embedded Videos Glitch When Published for MP4

I have several storyline files that were set so that they would be able to be played as an MP4. 
I have videos and images in the slides as well as additional text and graphics. 
When I publish to MP4, the videos have glitches in them. Like little hiccups and pauses.

Additionally, the images have an emphasis added to them to grow and some will randomly grow faster than designed. I have heard this was an issue, so we can deal with that, but I can't find any solution or guidance on the video issue.

We are using handbrake to reduce the size of the videos and then importing them into Storyline. The files are all MP4. 

I have tried to remove all of the emphasis to see if that would help, it did not. 

I also tried to use the _NOPROCESS_  at the end of the file name and ensured compression was set to none in the video options. I am publishing using the same dimensions as the project. Using Very High quality as my setting. 

Please help. This makes no sense. I have published videos inside of videos before and this has never happened.