I've found that another very useful setting that should probably be included with this type of interactive video, is to ensure that the Slide Properties for the Base Layer slide containing the video, is set to "Reset to initial state" when revisiting (on the cog wheel, bottom right).
I discovered when creating this type of content that if a user started viewing the video, exited before it reached the end and then went back to view it again, the video would continue playing from where it left off, but the intervening time spent away from the video would be counted on the base layer's timeline. This completely destroyed the synching of the cue points (and hence the appearance of subsequent messages on the layers).
I tried all manner of means to try and get the video to reset so that it started from scratch again in these circumstances, including adding a trigger to restart the course if the user clicked the exit button to leave the video, but nothing worked satisfactorily until I changed that Slide Properties setting. Now there are no more issues.