Great to hear that you were able to resolve it!!
One way minimize potential issues like that, is to let it play through the scene completely before doing something else in the animation. This is because Flash toy sync doesn’t actually know what is going on in the animation. It just knows what elements there are as well as their current frames and their total frames. It then makes assumptions based on that information for generating the different scenes.
I’m planning on adding more information like this to the github repo wiki, so it’s great knowing what kind of issues people are having.