Hi Daniel!
Happy to help with this!
Testing the design on my end, in the current version of Storyline 360, I was unable to replicate the same behavior. With a video added to a slide, video controls disabled, and the seek-bar enabled, the video relies upon the slide timeline to progress. When the timeline of the slide pauses or changes, so does the video.
It would be helpful to have a closer look at the .story file that's giving you trouble. Would you be comfortable sharing a copy here in the discussion or privately through a support case?
We'll delete it from our system as soon as troubleshooting is complete!