I tried to recreate this situation but everything worked great.
Here is a sample app for this situation:
347 - Word Highlight.zip

The text highlight starts a little later then the audio file. The element A in this sample app is the ball.

I tried to recreate this situation but everything worked great.
Here is a sample app for this situation:
347 - Word Highlight.zip

The text highlight starts a little later then the audio file. The element A in this sample app is the ball.

I tried to recreate this situation but everything is working as it great. Neither one of the action sets is disappearing.

Adding or deleting a frame it doesn't do anything to the shape elements. One thing that I noticed and forwarded to our lead developer was that the line shape is changing it's position when I switch from Design Mode to Interact Mode. 

I downloaded app 118. I saw the global counter on page 1, I navigated to page 1,2,3. ( I added on page 3 for the text element (with the narration) the target for the App counter because it wasn't set) went back to page 1, cleared the cache. The result: the global counter is intact, the condition for the text element on page 3 is working.

Could you tell me if you are using the Shake behavior on any pages for the "118-..." app from your Dropbox. I will take a look at it.

I was able to recreate this situation, and passed that information along to our lead developer. Thank you for the feedback.

Is it not working for you in Interact mode or InteractPlayer?
I created a sample app and it's working for me:
110 - Shake behavior.zip

The problem here was that you made the FadeOutIn to Replay one time, so after the first time the behavior is triggered, it will replay one more time. That will take 1 second but you have the Hide behavior set to 500ms so the Hide behavior will interrupt the FadeOutIn behavior.