David,
Now I had a chance to look a little more into your file and your problem.
And I've got it running now! I uploaded my modified version to https://adobe.ly/2WWZrZs.
Let me tell you first: You shouldn't be using Scenes. Instead develop your 'scenes' as seperate fla/swf files and load/unload them as SWF into a lead FLA document.
There is a snippet in ActionScript => Load and Unload => Click to Load/Unload SWF or Image. For a more handcoded spproach with steeper learning curve you could look into the AS3 Classes Loader and LoaderInfo. In my AS3 past the tutorials of RepublicOfCode have often helped me to get on with more complex AS3 subjects. So there is an introductory tutorial on Using the AS3 Loader Class.
This approach gives you smaller file sizes, easier editing through smaller units and more flexibility in setting up/combining trainings from a pool of SWFs.
The general disadvantages of Scenes are nicely summarized under How to work with scenes in Animate CC . See "Disadvantages of scenes".
Okay, back to your file.
In your fifth scene (Log-In to MasterControl) was an error. You've added an EventListener to an object which didn't exist (in that frame).
button_2goingcopy4.addEventListener(MouseEvent.CLICK, fl_ClickToGoToScene_5);
Instead it should be
button_2_forgoingscene3.addEventListener(MouseEvent.CLICK, fl_ClickToGoToScene_5);
This might have been the sole culprit. I'm not sure though. Because this error occured first in frame 1650 and doesn't fully explain why the playhead stopped already in frame 98 (your test setting) and as well in frame 1.
What I additionally did was to delete all reduntant frames in each scene (apart from the very last) which followed after your frames with stop() and gotoAndPlay() code to navigate to the next scene. These were in some cases several thousand frames. Pardon me, but this is madness to work so sloppy.
And I renamed your scenes (again apart from the very last one) to more descriptive titles in Window = Scene. This of course was not a real problem, I mention it in case you wonder about the new naming policy in my modified file linked above. Nevertheless take it as a suggestion from me.
Hope this helps
Klaus