If you are dynamically creating objects or adding them (using addChild) then they lose their grip on the timeline. You need to anchor/add them to objects that have a solid home in the timeline - as in objects that are manually placed in the timeline.
Before you become overly fond of the use of scenes you should try to avoid using them. They work fine for animators who work on lengthy animated pieces that flow from one to the next but for anything that involves navigation scenes can be very problematic. It is better to just use one scene and either spread things out along the timeline and/or use movieclips where you control their visibility. When you publish a file, all the scenes are scrunched into one timeline anyways so there is no benefit beyond providing a form of content isolation.