Don't use scenes. Scenes are a leftover methodology from the earliest versions of Flash. They serve no useful purpose and can cause any number of problems. Just say "NO" to scenes.
In any case, when you test the problematic movie do you get any error messages? Can you show us an example of one of these problematic movies?
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Scenes are very useful, historically for animators to be able to quickly preview a section of the whole animation, without having to always play from the start.
For applications, I've used scene as an easy way to layout major sections of my apps. There are alternate approaches, such as always using code to add a movieclip or a SWC to the stage when you need it, and I do work that way too.
Back to your problem, can you post an example FLA for us to try?
Pardon my ignorance, but there are no options to upload a file here. If there is a way to share the file then please do let me know and I will do so. I have put a link to the folder in my onedrive and shared it with you. Hopefully the problem can be resolved.